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- .gitattributes +305 -0
- grid_sampling/grid8_4d/common/config/grid_config.json +62 -0
- grid_sampling/grid8_4d/common/grid/grid_axis_1d_deg.npy +3 -0
- grid_sampling/grid8_4d/common/grid/grid_axis_1d_rad.npy +3 -0
- grid_sampling/grid8_4d/common/grid/grid_points_4d_rad.csv +0 -0
- grid_sampling/grid8_4d/common/metadata/initial_frame_search_overview.json +77 -0
- grid_sampling/grid8_4d/gly_gly/matches/grid_point_matches.csv +0 -0
- grid_sampling/grid8_4d/gly_gly/matches/grid_point_occupancy.csv +0 -0
- grid_sampling/grid8_4d/gly_gly/metadata/initial_frame_search_summary.json +15 -0
- grid_sampling/grid8_4d/gly_gly/metadata/trajectory_scan_summary.csv +5 -0
- grid_sampling/grid8_4d/gly_gly/metadata/trajectory_sources_used.csv +5 -0
- grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/init_structures/gly_gly_grid_0000_0.pdb +46 -0
- grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/init_structures/gly_gly_grid_0001_0.pdb +46 -0
- grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/init_structures/gly_gly_grid_0004_0.pdb +46 -0
- grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/init_structures/gly_gly_grid_0006_0.pdb +46 -0
- grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/init_structures/gly_gly_grid_0007_0.pdb +46 -0
- grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/init_structures/gly_gly_grid_0008_0.pdb +46 -0
- grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/init_structures/gly_gly_grid_0011_0.pdb +46 -0
- grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/init_structures/gly_gly_grid_0015_0.pdb +46 -0
- grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/init_structures/gly_gly_grid_0016_0.pdb +46 -0
- grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/init_structures/gly_gly_grid_0018_0.pdb +46 -0
- grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/init_structures/gly_gly_grid_0019_0.pdb +46 -0
- grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/init_structures/gly_gly_grid_0020_0.pdb +46 -0
- grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/init_structures/gly_gly_grid_0041_0.pdb +46 -0
- grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/init_structures/gly_gly_grid_0042_0.pdb +46 -0
- grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/init_structures/gly_gly_grid_0046_0.pdb +46 -0
- grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/init_structures/gly_gly_grid_0047_0.pdb +46 -0
- grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/init_structures/gly_gly_grid_0048_0.pdb +46 -0
- grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/init_structures/gly_gly_grid_0052_0.pdb +46 -0
- grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/init_structures/gly_gly_grid_0054_0.pdb +46 -0
- grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/init_structures/gly_gly_grid_0056_0.pdb +46 -0
- grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/init_structures/gly_gly_grid_0059_0.pdb +46 -0
- grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/init_structures/gly_gly_grid_0063_0.pdb +46 -0
- grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/init_structures/gly_gly_grid_0080_0.pdb +46 -0
- grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/init_structures/gly_gly_grid_0083_0.pdb +46 -0
- grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/init_structures/gly_gly_grid_0087_0.pdb +46 -0
- grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/init_structures/gly_gly_grid_0105_0.pdb +46 -0
- grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/init_structures/gly_gly_grid_0108_0.pdb +46 -0
- grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/init_structures/gly_gly_grid_0111_0.pdb +46 -0
- grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/init_structures/gly_gly_grid_0120_0.pdb +46 -0
- grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/init_structures/gly_gly_grid_0147_0.pdb +46 -0
- grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/init_structures/gly_gly_grid_0148_0.pdb +46 -0
- grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/init_structures/gly_gly_grid_0150_0.pdb +46 -0
- grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/init_structures/gly_gly_grid_0196_0.pdb +46 -0
- grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/init_structures/gly_gly_grid_0200_0.pdb +46 -0
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- grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/init_structures/gly_gly_grid_0210_0.pdb +46 -0
- grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/init_structures/gly_gly_grid_0215_0.pdb +46 -0
- grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/init_structures/gly_gly_grid_0232_0.pdb +46 -0
- grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/init_structures/gly_gly_grid_0235_0.pdb +46 -0
.gitattributes
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grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/trajectories/gly_gly_grid_0721_0.xtc filter=lfs diff=lfs merge=lfs -text
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grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/trajectories/gly_gly_grid_1455_0.xtc filter=lfs diff=lfs merge=lfs -text
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grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/trajectories/gly_gly_grid_2866_0.xtc filter=lfs diff=lfs merge=lfs -text
|
| 2605 |
+
grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/trajectories/gly_gly_grid_3844_0.xtc filter=lfs diff=lfs merge=lfs -text
|
| 2606 |
+
grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/trajectories/gly_gly_grid_0952_0.xtc filter=lfs diff=lfs merge=lfs -text
|
| 2607 |
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grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/trajectories/gly_gly_grid_3799_0.xtc filter=lfs diff=lfs merge=lfs -text
|
| 2608 |
+
grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/trajectories/gly_gly_grid_2928_0.xtc filter=lfs diff=lfs merge=lfs -text
|
| 2609 |
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grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/trajectories/gly_gly_grid_1005_0.xtc filter=lfs diff=lfs merge=lfs -text
|
| 2610 |
+
grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/trajectories/gly_gly_grid_3584_0.xtc filter=lfs diff=lfs merge=lfs -text
|
| 2611 |
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grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/trajectories/gly_gly_grid_1469_0.xtc filter=lfs diff=lfs merge=lfs -text
|
| 2612 |
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grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/trajectories/gly_gly_grid_0004_0.xtc filter=lfs diff=lfs merge=lfs -text
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| 2613 |
+
grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/trajectories/gly_gly_grid_4031_0.xtc filter=lfs diff=lfs merge=lfs -text
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| 2614 |
+
grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/trajectories/gly_gly_grid_0747_0.xtc filter=lfs diff=lfs merge=lfs -text
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| 2615 |
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grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/trajectories/gly_gly_grid_1412_0.xtc filter=lfs diff=lfs merge=lfs -text
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| 2616 |
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grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/trajectories/gly_gly_grid_1274_0.xtc filter=lfs diff=lfs merge=lfs -text
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| 2617 |
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grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/trajectories/gly_gly_grid_3888_0.xtc filter=lfs diff=lfs merge=lfs -text
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| 2618 |
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grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/trajectories/gly_gly_grid_1428_0.xtc filter=lfs diff=lfs merge=lfs -text
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| 2619 |
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grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/trajectories/gly_gly_grid_1038_0.xtc filter=lfs diff=lfs merge=lfs -text
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| 2620 |
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grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/trajectories/gly_gly_grid_0587_0.xtc filter=lfs diff=lfs merge=lfs -text
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| 2621 |
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grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/trajectories/gly_gly_grid_0725_0.xtc filter=lfs diff=lfs merge=lfs -text
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| 2622 |
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grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/trajectories/gly_gly_grid_0791_0.xtc filter=lfs diff=lfs merge=lfs -text
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| 2623 |
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grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/trajectories/gly_gly_grid_1267_0.xtc filter=lfs diff=lfs merge=lfs -text
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| 2624 |
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grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/trajectories/gly_gly_grid_2867_0.xtc filter=lfs diff=lfs merge=lfs -text
|
| 2625 |
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grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/trajectories/gly_gly_grid_3309_0.xtc filter=lfs diff=lfs merge=lfs -text
|
| 2626 |
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grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/trajectories/gly_gly_grid_0632_0.xtc filter=lfs diff=lfs merge=lfs -text
|
| 2627 |
+
grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/trajectories/gly_gly_grid_0456_0.xtc filter=lfs diff=lfs merge=lfs -text
|
| 2628 |
+
grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/trajectories/gly_gly_grid_1022_0.xtc filter=lfs diff=lfs merge=lfs -text
|
| 2629 |
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grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/trajectories/gly_gly_grid_2815_0.xtc filter=lfs diff=lfs merge=lfs -text
|
| 2630 |
+
grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/trajectories/gly_gly_grid_0520_0.xtc filter=lfs diff=lfs merge=lfs -text
|
| 2631 |
+
grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/trajectories/gly_gly_grid_1459_0.xtc filter=lfs diff=lfs merge=lfs -text
|
| 2632 |
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grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/trajectories/gly_gly_grid_1001_0.xtc filter=lfs diff=lfs merge=lfs -text
|
| 2633 |
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grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/trajectories/gly_gly_grid_0080_0.xtc filter=lfs diff=lfs merge=lfs -text
|
| 2634 |
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grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/trajectories/gly_gly_grid_1159_0.xtc filter=lfs diff=lfs merge=lfs -text
|
| 2635 |
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grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/trajectories/gly_gly_grid_3117_0.xtc filter=lfs diff=lfs merge=lfs -text
|
| 2636 |
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grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/trajectories/gly_gly_grid_3140_0.xtc filter=lfs diff=lfs merge=lfs -text
|
| 2637 |
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grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/trajectories/gly_gly_grid_0533_0.xtc filter=lfs diff=lfs merge=lfs -text
|
| 2638 |
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grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/trajectories/gly_gly_grid_3576_0.xtc filter=lfs diff=lfs merge=lfs -text
|
| 2639 |
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grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/trajectories/gly_gly_grid_1523_0.xtc filter=lfs diff=lfs merge=lfs -text
|
| 2640 |
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grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/trajectories/gly_gly_grid_3087_0.xtc filter=lfs diff=lfs merge=lfs -text
|
| 2641 |
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grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/trajectories/gly_gly_grid_1200_0.xtc filter=lfs diff=lfs merge=lfs -text
|
| 2642 |
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grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/trajectories/gly_gly_grid_2833_0.xtc filter=lfs diff=lfs merge=lfs -text
|
| 2643 |
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grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/trajectories/gly_gly_grid_0966_0.xtc filter=lfs diff=lfs merge=lfs -text
|
| 2644 |
+
grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/trajectories/gly_gly_grid_2695_0.xtc filter=lfs diff=lfs merge=lfs -text
|
| 2645 |
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grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/trajectories/gly_gly_grid_0767_0.xtc filter=lfs diff=lfs merge=lfs -text
|
| 2646 |
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grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/trajectories/gly_gly_grid_3575_0.xtc filter=lfs diff=lfs merge=lfs -text
|
| 2647 |
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grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/trajectories/gly_gly_grid_3124_0.xtc filter=lfs diff=lfs merge=lfs -text
|
| 2648 |
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grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/trajectories/gly_gly_grid_2824_0.xtc filter=lfs diff=lfs merge=lfs -text
|
| 2649 |
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grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/trajectories/gly_gly_grid_3080_0.xtc filter=lfs diff=lfs merge=lfs -text
|
| 2650 |
+
grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/trajectories/gly_gly_grid_4090_0.xtc filter=lfs diff=lfs merge=lfs -text
|
| 2651 |
+
grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/trajectories/gly_gly_grid_1296_0.xtc filter=lfs diff=lfs merge=lfs -text
|
| 2652 |
+
grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/trajectories/gly_gly_grid_3054_0.xtc filter=lfs diff=lfs merge=lfs -text
|
| 2653 |
+
grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/trajectories/gly_gly_grid_2639_0.xtc filter=lfs diff=lfs merge=lfs -text
|
| 2654 |
+
grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/trajectories/gly_gly_grid_3007_0.xtc filter=lfs diff=lfs merge=lfs -text
|
| 2655 |
+
grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/trajectories/gly_gly_grid_3328_0.xtc filter=lfs diff=lfs merge=lfs -text
|
| 2656 |
+
grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/trajectories/gly_gly_grid_1366_0.xtc filter=lfs diff=lfs merge=lfs -text
|
| 2657 |
+
grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/trajectories/gly_gly_grid_4050_0.xtc filter=lfs diff=lfs merge=lfs -text
|
| 2658 |
+
grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/trajectories/gly_gly_grid_3199_0.xtc filter=lfs diff=lfs merge=lfs -text
|
| 2659 |
+
grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/trajectories/gly_gly_grid_2896_0.xtc filter=lfs diff=lfs merge=lfs -text
|
| 2660 |
+
grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/trajectories/gly_gly_grid_0530_0.xtc filter=lfs diff=lfs merge=lfs -text
|
| 2661 |
+
grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/trajectories/gly_gly_grid_0364_0.xtc filter=lfs diff=lfs merge=lfs -text
|
| 2662 |
+
grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/trajectories/gly_gly_grid_3026_0.xtc filter=lfs diff=lfs merge=lfs -text
|
| 2663 |
+
grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/trajectories/gly_gly_grid_2799_0.xtc filter=lfs diff=lfs merge=lfs -text
|
| 2664 |
+
grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/trajectories/gly_gly_grid_4078_0.xtc filter=lfs diff=lfs merge=lfs -text
|
| 2665 |
+
grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/trajectories/gly_gly_grid_3008_0.xtc filter=lfs diff=lfs merge=lfs -text
|
| 2666 |
+
grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/trajectories/gly_gly_grid_1975_0.xtc filter=lfs diff=lfs merge=lfs -text
|
| 2667 |
+
grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/trajectories/gly_gly_grid_0575_0.xtc filter=lfs diff=lfs merge=lfs -text
|
| 2668 |
+
grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/trajectories/gly_gly_grid_1073_0.xtc filter=lfs diff=lfs merge=lfs -text
|
| 2669 |
+
grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/trajectories/gly_gly_grid_0552_0.xtc filter=lfs diff=lfs merge=lfs -text
|
grid_sampling/grid8_4d/common/config/grid_config.json
ADDED
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+
{
|
| 2 |
+
"grid_points_per_dimension": 8,
|
| 3 |
+
"num_dimensions": 4,
|
| 4 |
+
"num_grid_points_total": 4096,
|
| 5 |
+
"rc_names": [
|
| 6 |
+
"phi1",
|
| 7 |
+
"psi1",
|
| 8 |
+
"phi2",
|
| 9 |
+
"psi2"
|
| 10 |
+
],
|
| 11 |
+
"periodic_range_rad": [
|
| 12 |
+
-3.141592653589793,
|
| 13 |
+
3.141592653589793
|
| 14 |
+
],
|
| 15 |
+
"grid_spacing_rad": 0.7853981633974483,
|
| 16 |
+
"grid_spacing_deg": 45.0,
|
| 17 |
+
"max_assignment_distance_rad": 0.2617993877991494,
|
| 18 |
+
"max_assignment_distance_deg": 14.999999999999998,
|
| 19 |
+
"max_points_per_gridpoint": 10,
|
| 20 |
+
"trajectory_sources": [
|
| 21 |
+
{
|
| 22 |
+
"molecule": "ALA-ALA",
|
| 23 |
+
"run_dir": "/home/vanib/scratch/md_data/ala_ala_prod_from_gpu_smoke_70ns_freq1_20260302_235247",
|
| 24 |
+
"xtc_path": "/home/vanib/scratch/md_data/ala_ala_prod_from_gpu_smoke_70ns_freq1_20260302_235247/equilNPT_2_protein_prod_70ns_f1.xtc"
|
| 25 |
+
},
|
| 26 |
+
{
|
| 27 |
+
"molecule": "ALA-ALA",
|
| 28 |
+
"run_dir": "/home/vanib/scratch/md_data/ala_ala_prod_continue_130ns_freq1_20260303_045322",
|
| 29 |
+
"xtc_path": "/home/vanib/scratch/md_data/ala_ala_prod_continue_130ns_freq1_20260303_045322/equilNPT_2_protein_prod_cont130ns_f1.xtc"
|
| 30 |
+
},
|
| 31 |
+
{
|
| 32 |
+
"molecule": "ALA-GLY",
|
| 33 |
+
"run_dir": "/home/vanib/scratch/md_data/ala_gly_gpu_70ns_f1_20260302_234427",
|
| 34 |
+
"xtc_path": "/home/vanib/scratch/md_data/ala_gly_gpu_70ns_f1_20260302_234427/capped_ala_gly.xtc"
|
| 35 |
+
},
|
| 36 |
+
{
|
| 37 |
+
"molecule": "ALA-GLY",
|
| 38 |
+
"run_dir": "/home/vanib/scratch/md_data/ala_gly_continue_130ns_freq1_20260303_045324",
|
| 39 |
+
"xtc_path": "/home/vanib/scratch/md_data/ala_gly_continue_130ns_freq1_20260303_045324/capped_ala_gly_cont130ns_f1.xtc"
|
| 40 |
+
},
|
| 41 |
+
{
|
| 42 |
+
"molecule": "GLY-GLY",
|
| 43 |
+
"run_dir": "/home/vanib/scratch/md_data/gly_gly_gpu_70ns_f1_20260302_234427",
|
| 44 |
+
"xtc_path": "/home/vanib/scratch/md_data/gly_gly_gpu_70ns_f1_20260302_234427/capped_gly_gly.xtc"
|
| 45 |
+
},
|
| 46 |
+
{
|
| 47 |
+
"molecule": "GLY-GLY",
|
| 48 |
+
"run_dir": "/home/vanib/scratch/md_data/gly_gly_continue_130ns_freq1_20260303_045324",
|
| 49 |
+
"xtc_path": "/home/vanib/scratch/md_data/gly_gly_continue_130ns_freq1_20260303_045324/capped_gly_gly_cont130ns_f1.xtc"
|
| 50 |
+
},
|
| 51 |
+
{
|
| 52 |
+
"molecule": "GLY-ALA",
|
| 53 |
+
"run_dir": "/home/vanib/scratch/md_data/gly_ala_gpu_70ns_f1_20260302_234427",
|
| 54 |
+
"xtc_path": "/home/vanib/scratch/md_data/gly_ala_gpu_70ns_f1_20260302_234427/capped_gly_ala.xtc"
|
| 55 |
+
},
|
| 56 |
+
{
|
| 57 |
+
"molecule": "GLY-ALA",
|
| 58 |
+
"run_dir": "/home/vanib/scratch/md_data/gly_ala_continue_130ns_freq1_20260303_045347",
|
| 59 |
+
"xtc_path": "/home/vanib/scratch/md_data/gly_ala_continue_130ns_freq1_20260303_045347/capped_gly_ala_cont130ns_f1.xtc"
|
| 60 |
+
}
|
| 61 |
+
]
|
| 62 |
+
}
|
grid_sampling/grid8_4d/common/grid/grid_axis_1d_deg.npy
ADDED
|
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| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:a224bec74dd9142fa460935a62a457506c8bacc9451b0e03d905668fbf97514c
|
| 3 |
+
size 192
|
grid_sampling/grid8_4d/common/grid/grid_axis_1d_rad.npy
ADDED
|
@@ -0,0 +1,3 @@
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|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:2c3c897b6db98981aee7c4e7290d7813425504fbc45d7c6b1fa26834921cbfbd
|
| 3 |
+
size 192
|
grid_sampling/grid8_4d/common/grid/grid_points_4d_rad.csv
ADDED
|
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|
grid_sampling/grid8_4d/common/metadata/initial_frame_search_overview.json
ADDED
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"config": "/gpfs/scratchfs01/site/u/vanib/md_data/enhanced_sampling/grid8_4d/common/config/grid_config.json",
|
| 3 |
+
"data_root": "/gpfs/scratchfs01/site/u/vanib/md_data",
|
| 4 |
+
"enhanced_root": "/gpfs/scratchfs01/site/u/vanib/md_data/enhanced_sampling/grid8_4d",
|
| 5 |
+
"grid_points_per_dimension": 8,
|
| 6 |
+
"num_grid_points_total": 4096,
|
| 7 |
+
"grid_spacing_rad": 0.7853981633974483,
|
| 8 |
+
"max_assignment_distance_rad": 0.2617993877991494,
|
| 9 |
+
"max_points_per_gridpoint": 10,
|
| 10 |
+
"stride": 200,
|
| 11 |
+
"chunk_size": 20000,
|
| 12 |
+
"max_sampled_frames_per_trajectory": null,
|
| 13 |
+
"skip_known_run_globs": false,
|
| 14 |
+
"write_init_pdbs": false,
|
| 15 |
+
"molecules": {
|
| 16 |
+
"ALA-ALA": {
|
| 17 |
+
"molecule": "ALA-ALA",
|
| 18 |
+
"molecule_tag": "ala_ala",
|
| 19 |
+
"num_trajectories": 4,
|
| 20 |
+
"num_grid_points": 4096,
|
| 21 |
+
"occupied_grid_points": 405,
|
| 22 |
+
"grid_coverage_fraction": 0.098876953125,
|
| 23 |
+
"total_selected_frames": 2234,
|
| 24 |
+
"max_points_per_gridpoint": 10,
|
| 25 |
+
"max_assignment_distance_rad": 0.2617993877991494,
|
| 26 |
+
"stride": 200,
|
| 27 |
+
"chunk_size": 20000,
|
| 28 |
+
"max_sampled_frames_per_trajectory": null,
|
| 29 |
+
"write_init_pdbs": false
|
| 30 |
+
},
|
| 31 |
+
"ALA-GLY": {
|
| 32 |
+
"molecule": "ALA-GLY",
|
| 33 |
+
"molecule_tag": "ala_gly",
|
| 34 |
+
"num_trajectories": 4,
|
| 35 |
+
"num_grid_points": 4096,
|
| 36 |
+
"occupied_grid_points": 654,
|
| 37 |
+
"grid_coverage_fraction": 0.15966796875,
|
| 38 |
+
"total_selected_frames": 3399,
|
| 39 |
+
"max_points_per_gridpoint": 10,
|
| 40 |
+
"max_assignment_distance_rad": 0.2617993877991494,
|
| 41 |
+
"stride": 200,
|
| 42 |
+
"chunk_size": 20000,
|
| 43 |
+
"max_sampled_frames_per_trajectory": null,
|
| 44 |
+
"write_init_pdbs": false
|
| 45 |
+
},
|
| 46 |
+
"GLY-ALA": {
|
| 47 |
+
"molecule": "GLY-ALA",
|
| 48 |
+
"molecule_tag": "gly_ala",
|
| 49 |
+
"num_trajectories": 4,
|
| 50 |
+
"num_grid_points": 4096,
|
| 51 |
+
"occupied_grid_points": 690,
|
| 52 |
+
"grid_coverage_fraction": 0.16845703125,
|
| 53 |
+
"total_selected_frames": 3547,
|
| 54 |
+
"max_points_per_gridpoint": 10,
|
| 55 |
+
"max_assignment_distance_rad": 0.2617993877991494,
|
| 56 |
+
"stride": 200,
|
| 57 |
+
"chunk_size": 20000,
|
| 58 |
+
"max_sampled_frames_per_trajectory": null,
|
| 59 |
+
"write_init_pdbs": false
|
| 60 |
+
},
|
| 61 |
+
"GLY-GLY": {
|
| 62 |
+
"molecule": "GLY-GLY",
|
| 63 |
+
"molecule_tag": "gly_gly",
|
| 64 |
+
"num_trajectories": 4,
|
| 65 |
+
"num_grid_points": 4096,
|
| 66 |
+
"occupied_grid_points": 1129,
|
| 67 |
+
"grid_coverage_fraction": 0.275634765625,
|
| 68 |
+
"total_selected_frames": 5437,
|
| 69 |
+
"max_points_per_gridpoint": 10,
|
| 70 |
+
"max_assignment_distance_rad": 0.2617993877991494,
|
| 71 |
+
"stride": 200,
|
| 72 |
+
"chunk_size": 20000,
|
| 73 |
+
"max_sampled_frames_per_trajectory": null,
|
| 74 |
+
"write_init_pdbs": false
|
| 75 |
+
}
|
| 76 |
+
}
|
| 77 |
+
}
|
grid_sampling/grid8_4d/gly_gly/matches/grid_point_matches.csv
ADDED
|
The diff for this file is too large to render.
See raw diff
|
|
|
grid_sampling/grid8_4d/gly_gly/matches/grid_point_occupancy.csv
ADDED
|
The diff for this file is too large to render.
See raw diff
|
|
|
grid_sampling/grid8_4d/gly_gly/metadata/initial_frame_search_summary.json
ADDED
|
@@ -0,0 +1,15 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"molecule": "GLY-GLY",
|
| 3 |
+
"molecule_tag": "gly_gly",
|
| 4 |
+
"num_trajectories": 4,
|
| 5 |
+
"num_grid_points": 4096,
|
| 6 |
+
"occupied_grid_points": 1129,
|
| 7 |
+
"grid_coverage_fraction": 0.275634765625,
|
| 8 |
+
"total_selected_frames": 5437,
|
| 9 |
+
"max_points_per_gridpoint": 10,
|
| 10 |
+
"max_assignment_distance_rad": 0.2617993877991494,
|
| 11 |
+
"stride": 200,
|
| 12 |
+
"chunk_size": 20000,
|
| 13 |
+
"max_sampled_frames_per_trajectory": null,
|
| 14 |
+
"write_init_pdbs": false
|
| 15 |
+
}
|
grid_sampling/grid8_4d/gly_gly/metadata/trajectory_scan_summary.csv
ADDED
|
@@ -0,0 +1,5 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
molecule,run_dir,xtc_path,topology_source_pdb,sampled_frames_scanned,frames_within_cutoff,stride,chunk_size
|
| 2 |
+
GLY-GLY,/gpfs/scratchfs01/site/u/vanib/md_data/gly_gly_continue_130ns_freq1_20260303_045022,/gpfs/scratchfs01/site/u/vanib/md_data/gly_gly_continue_130ns_freq1_20260303_045022/capped_gly_gly_cont130ns_f1.xtc,/gpfs/scratchfs01/site/u/vanib/md_data/gly_gly_gpu_70ns_f1_20260302_233842/capped_gly_gly_fixed_0.pdb,2,0,200,20000
|
| 3 |
+
GLY-GLY,/gpfs/scratchfs01/site/u/vanib/md_data/gly_gly_continue_130ns_freq1_20260303_045324,/gpfs/scratchfs01/site/u/vanib/md_data/gly_gly_continue_130ns_freq1_20260303_045324/capped_gly_gly_cont130ns_f1.xtc,/gpfs/scratchfs01/site/u/vanib/md_data/gly_gly_gpu_70ns_f1_20260302_233842/capped_gly_gly_fixed_0.pdb,59085,4996,200,20000
|
| 4 |
+
GLY-GLY,/gpfs/scratchfs01/site/u/vanib/md_data/gly_gly_gpu_70ns_f1_20260302_233842,/gpfs/scratchfs01/site/u/vanib/md_data/gly_gly_gpu_70ns_f1_20260302_233842/capped_gly_gly.xtc,/gpfs/scratchfs01/site/u/vanib/md_data/gly_gly_gpu_70ns_f1_20260302_233842/capped_gly_gly_fixed_0.pdb,1565,126,200,20000
|
| 5 |
+
GLY-GLY,/gpfs/scratchfs01/site/u/vanib/md_data/gly_gly_gpu_70ns_f1_20260302_234427,/gpfs/scratchfs01/site/u/vanib/md_data/gly_gly_gpu_70ns_f1_20260302_234427/capped_gly_gly.xtc,/gpfs/scratchfs01/site/u/vanib/md_data/gly_gly_gpu_70ns_f1_20260302_233842/capped_gly_gly_fixed_0.pdb,175000,14218,200,20000
|
grid_sampling/grid8_4d/gly_gly/metadata/trajectory_sources_used.csv
ADDED
|
@@ -0,0 +1,5 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
molecule,run_dir,xtc_path,topology_source_pdb,topology_atoms
|
| 2 |
+
GLY-GLY,/gpfs/scratchfs01/site/u/vanib/md_data/gly_gly_continue_130ns_freq1_20260303_045022,/gpfs/scratchfs01/site/u/vanib/md_data/gly_gly_continue_130ns_freq1_20260303_045022/capped_gly_gly_cont130ns_f1.xtc,/gpfs/scratchfs01/site/u/vanib/md_data/gly_gly_gpu_70ns_f1_20260302_233842/capped_gly_gly_fixed_0.pdb,26
|
| 3 |
+
GLY-GLY,/gpfs/scratchfs01/site/u/vanib/md_data/gly_gly_continue_130ns_freq1_20260303_045324,/gpfs/scratchfs01/site/u/vanib/md_data/gly_gly_continue_130ns_freq1_20260303_045324/capped_gly_gly_cont130ns_f1.xtc,/gpfs/scratchfs01/site/u/vanib/md_data/gly_gly_gpu_70ns_f1_20260302_233842/capped_gly_gly_fixed_0.pdb,26
|
| 4 |
+
GLY-GLY,/gpfs/scratchfs01/site/u/vanib/md_data/gly_gly_gpu_70ns_f1_20260302_233842,/gpfs/scratchfs01/site/u/vanib/md_data/gly_gly_gpu_70ns_f1_20260302_233842/capped_gly_gly.xtc,/gpfs/scratchfs01/site/u/vanib/md_data/gly_gly_gpu_70ns_f1_20260302_233842/capped_gly_gly_fixed_0.pdb,26
|
| 5 |
+
GLY-GLY,/gpfs/scratchfs01/site/u/vanib/md_data/gly_gly_gpu_70ns_f1_20260302_234427,/gpfs/scratchfs01/site/u/vanib/md_data/gly_gly_gpu_70ns_f1_20260302_234427/capped_gly_gly.xtc,/gpfs/scratchfs01/site/u/vanib/md_data/gly_gly_gpu_70ns_f1_20260302_233842/capped_gly_gly_fixed_0.pdb,26
|
grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/init_structures/gly_gly_grid_0000_0.pdb
ADDED
|
@@ -0,0 +1,46 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
REMARK 1 CREATED WITH MDTraj 1.10.3, 2026-03-03
|
| 2 |
+
CRYST1 21.808 21.808 21.808 90.00 90.00 90.00 P 1 1
|
| 3 |
+
MODEL 0
|
| 4 |
+
ATOM 1 H1 ACE A 1 9.840 17.190 12.620 1.00 0.00 H
|
| 5 |
+
ATOM 2 CH3 ACE A 1 9.850 17.540 11.580 1.00 0.00 C
|
| 6 |
+
ATOM 3 H2 ACE A 1 8.970 18.160 11.450 1.00 0.00 H
|
| 7 |
+
ATOM 4 H3 ACE A 1 9.970 16.670 10.930 1.00 0.00 H
|
| 8 |
+
ATOM 5 C ACE A 1 10.950 18.530 11.380 1.00 0.00 C
|
| 9 |
+
ATOM 6 O ACE A 1 11.490 19.080 12.340 1.00 0.00 O
|
| 10 |
+
ATOM 7 N GLY A 2 11.260 18.710 10.100 1.00 0.00 N
|
| 11 |
+
ATOM 8 H GLY A 2 10.630 18.350 9.390 1.00 0.00 H
|
| 12 |
+
ATOM 9 CA GLY A 2 12.310 19.600 9.660 1.00 0.00 C
|
| 13 |
+
ATOM 10 HA2 GLY A 2 12.310 20.560 10.170 1.00 0.00 H
|
| 14 |
+
ATOM 11 HA3 GLY A 2 13.300 19.170 9.840 1.00 0.00 H
|
| 15 |
+
ATOM 12 C GLY A 2 12.170 20.040 8.190 1.00 0.00 C
|
| 16 |
+
ATOM 13 O GLY A 2 11.010 20.170 7.730 1.00 0.00 O
|
| 17 |
+
ATOM 14 N GLY A 3 13.280 20.380 7.490 1.00 0.00 N
|
| 18 |
+
ATOM 15 H GLY A 3 14.160 20.260 7.980 1.00 0.00 H
|
| 19 |
+
ATOM 16 CA GLY A 3 13.180 20.630 5.970 1.00 0.00 C
|
| 20 |
+
ATOM 17 HA2 GLY A 3 12.450 19.890 5.650 1.00 0.00 H
|
| 21 |
+
ATOM 18 HA3 GLY A 3 12.820 21.640 5.730 1.00 0.00 H
|
| 22 |
+
ATOM 19 C GLY A 3 14.520 20.360 5.300 1.00 0.00 C
|
| 23 |
+
ATOM 20 O GLY A 3 15.380 19.600 5.790 1.00 0.00 O
|
| 24 |
+
ATOM 21 N NME A 4 14.730 21.040 4.110 1.00 0.00 N
|
| 25 |
+
ATOM 22 H NME A 4 14.010 21.690 3.820 1.00 0.00 H
|
| 26 |
+
ATOM 23 C NME A 4 15.980 21.040 3.370 1.00 0.00 C
|
| 27 |
+
ATOM 24 H1 NME A 4 16.770 21.620 3.840 1.00 0.00 H
|
| 28 |
+
ATOM 25 H2 NME A 4 16.240 20.020 3.060 1.00 0.00 H
|
| 29 |
+
ATOM 26 H3 NME A 4 15.680 21.490 2.420 1.00 0.00 H
|
| 30 |
+
TER 27 NME A 4
|
| 31 |
+
ENDMDL
|
| 32 |
+
CONECT 1 2
|
| 33 |
+
CONECT 2 5 1 3 4
|
| 34 |
+
CONECT 3 2
|
| 35 |
+
CONECT 4 2
|
| 36 |
+
CONECT 5 2 6 7
|
| 37 |
+
CONECT 6 5
|
| 38 |
+
CONECT 7 5
|
| 39 |
+
CONECT 19 21
|
| 40 |
+
CONECT 21 19 23 22
|
| 41 |
+
CONECT 22 21
|
| 42 |
+
CONECT 23 24 25 26 21
|
| 43 |
+
CONECT 24 23
|
| 44 |
+
CONECT 25 23
|
| 45 |
+
CONECT 26 23
|
| 46 |
+
END
|
grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/init_structures/gly_gly_grid_0001_0.pdb
ADDED
|
@@ -0,0 +1,46 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
REMARK 1 CREATED WITH MDTraj 1.10.3, 2026-03-03
|
| 2 |
+
CRYST1 21.788 21.788 21.788 90.00 90.00 90.00 P 1 1
|
| 3 |
+
MODEL 0
|
| 4 |
+
ATOM 1 H1 ACE A 1 7.420 16.980 15.910 1.00 0.00 H
|
| 5 |
+
ATOM 2 CH3 ACE A 1 7.590 17.860 15.300 1.00 0.00 C
|
| 6 |
+
ATOM 3 H2 ACE A 1 6.650 18.210 14.890 1.00 0.00 H
|
| 7 |
+
ATOM 4 H3 ACE A 1 8.290 17.600 14.510 1.00 0.00 H
|
| 8 |
+
ATOM 5 C ACE A 1 8.250 19.030 16.070 1.00 0.00 C
|
| 9 |
+
ATOM 6 O ACE A 1 8.950 19.810 15.470 1.00 0.00 O
|
| 10 |
+
ATOM 7 N GLY A 2 8.240 18.870 17.420 1.00 0.00 N
|
| 11 |
+
ATOM 8 H GLY A 2 7.750 18.060 17.760 1.00 0.00 H
|
| 12 |
+
ATOM 9 CA GLY A 2 9.240 19.510 18.290 1.00 0.00 C
|
| 13 |
+
ATOM 10 HA2 GLY A 2 10.200 19.600 17.780 1.00 0.00 H
|
| 14 |
+
ATOM 11 HA3 GLY A 2 9.020 20.520 18.620 1.00 0.00 H
|
| 15 |
+
ATOM 12 C GLY A 2 9.370 18.690 19.590 1.00 0.00 C
|
| 16 |
+
ATOM 13 O GLY A 2 8.860 17.550 19.630 1.00 0.00 O
|
| 17 |
+
ATOM 14 N GLY A 3 9.880 19.290 20.710 1.00 0.00 N
|
| 18 |
+
ATOM 15 H GLY A 3 10.270 20.210 20.640 1.00 0.00 H
|
| 19 |
+
ATOM 16 CA GLY A 3 9.870 18.560 21.960 1.00 0.00 C
|
| 20 |
+
ATOM 17 HA2 GLY A 3 8.840 18.210 22.010 1.00 0.00 H
|
| 21 |
+
ATOM 18 HA3 GLY A 3 10.520 17.690 21.980 1.00 0.00 H
|
| 22 |
+
ATOM 19 C GLY A 3 10.100 19.530 23.180 1.00 0.00 C
|
| 23 |
+
ATOM 20 O GLY A 3 9.210 20.230 23.580 1.00 0.00 O
|
| 24 |
+
ATOM 21 N NME A 4 11.300 19.330 23.780 1.00 0.00 N
|
| 25 |
+
ATOM 22 H NME A 4 11.910 18.640 23.360 1.00 0.00 H
|
| 26 |
+
ATOM 23 C NME A 4 11.760 20.270 24.860 1.00 0.00 C
|
| 27 |
+
ATOM 24 H1 NME A 4 12.820 20.490 24.760 1.00 0.00 H
|
| 28 |
+
ATOM 25 H2 NME A 4 11.230 21.220 24.930 1.00 0.00 H
|
| 29 |
+
ATOM 26 H3 NME A 4 11.630 19.810 25.840 1.00 0.00 H
|
| 30 |
+
TER 27 NME A 4
|
| 31 |
+
ENDMDL
|
| 32 |
+
CONECT 1 2
|
| 33 |
+
CONECT 2 5 1 3 4
|
| 34 |
+
CONECT 3 2
|
| 35 |
+
CONECT 4 2
|
| 36 |
+
CONECT 5 2 6 7
|
| 37 |
+
CONECT 6 5
|
| 38 |
+
CONECT 7 5
|
| 39 |
+
CONECT 19 21
|
| 40 |
+
CONECT 21 19 23 22
|
| 41 |
+
CONECT 22 21
|
| 42 |
+
CONECT 23 24 25 26 21
|
| 43 |
+
CONECT 24 23
|
| 44 |
+
CONECT 25 23
|
| 45 |
+
CONECT 26 23
|
| 46 |
+
END
|
grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/init_structures/gly_gly_grid_0004_0.pdb
ADDED
|
@@ -0,0 +1,46 @@
|
|
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|
|
|
|
|
|
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|
|
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|
|
|
|
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|
|
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|
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|
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|
|
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|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
REMARK 1 CREATED WITH MDTraj 1.10.3, 2026-03-03
|
| 2 |
+
CRYST1 21.820 21.820 21.820 90.00 90.00 90.00 P 1 1
|
| 3 |
+
MODEL 0
|
| 4 |
+
ATOM 1 H1 ACE A 1 23.440 10.130 16.280 1.00 0.00 H
|
| 5 |
+
ATOM 2 CH3 ACE A 1 22.900 11.060 16.090 1.00 0.00 C
|
| 6 |
+
ATOM 3 H2 ACE A 1 22.600 11.120 15.040 1.00 0.00 H
|
| 7 |
+
ATOM 4 H3 ACE A 1 23.590 11.880 16.310 1.00 0.00 H
|
| 8 |
+
ATOM 5 C ACE A 1 21.660 11.080 16.950 1.00 0.00 C
|
| 9 |
+
ATOM 6 O ACE A 1 21.050 12.080 17.110 1.00 0.00 O
|
| 10 |
+
ATOM 7 N GLY A 2 21.420 9.960 17.570 1.00 0.00 N
|
| 11 |
+
ATOM 8 H GLY A 2 22.020 9.180 17.330 1.00 0.00 H
|
| 12 |
+
ATOM 9 CA GLY A 2 20.310 9.680 18.480 1.00 0.00 C
|
| 13 |
+
ATOM 10 HA2 GLY A 2 20.080 10.530 19.120 1.00 0.00 H
|
| 14 |
+
ATOM 11 HA3 GLY A 2 19.460 9.400 17.870 1.00 0.00 H
|
| 15 |
+
ATOM 12 C GLY A 2 20.650 8.520 19.420 1.00 0.00 C
|
| 16 |
+
ATOM 13 O GLY A 2 21.840 8.290 19.720 1.00 0.00 O
|
| 17 |
+
ATOM 14 N GLY A 3 19.660 7.830 19.930 1.00 0.00 N
|
| 18 |
+
ATOM 15 H GLY A 3 18.740 8.180 19.720 1.00 0.00 H
|
| 19 |
+
ATOM 16 CA GLY A 3 19.790 6.730 20.900 1.00 0.00 C
|
| 20 |
+
ATOM 17 HA2 GLY A 3 20.630 6.180 20.490 1.00 0.00 H
|
| 21 |
+
ATOM 18 HA3 GLY A 3 19.950 7.160 21.890 1.00 0.00 H
|
| 22 |
+
ATOM 19 C GLY A 3 18.630 5.740 20.910 1.00 0.00 C
|
| 23 |
+
ATOM 20 O GLY A 3 18.520 5.010 21.900 1.00 0.00 O
|
| 24 |
+
ATOM 21 N NME A 4 17.770 5.620 19.870 1.00 0.00 N
|
| 25 |
+
ATOM 22 H NME A 4 17.750 6.240 19.080 1.00 0.00 H
|
| 26 |
+
ATOM 23 C NME A 4 16.770 4.570 19.770 1.00 0.00 C
|
| 27 |
+
ATOM 24 H1 NME A 4 15.870 5.010 19.340 1.00 0.00 H
|
| 28 |
+
ATOM 25 H2 NME A 4 17.170 3.730 19.200 1.00 0.00 H
|
| 29 |
+
ATOM 26 H3 NME A 4 16.660 4.210 20.800 1.00 0.00 H
|
| 30 |
+
TER 27 NME A 4
|
| 31 |
+
ENDMDL
|
| 32 |
+
CONECT 1 2
|
| 33 |
+
CONECT 2 5 1 3 4
|
| 34 |
+
CONECT 3 2
|
| 35 |
+
CONECT 4 2
|
| 36 |
+
CONECT 5 2 6 7
|
| 37 |
+
CONECT 6 5
|
| 38 |
+
CONECT 7 5
|
| 39 |
+
CONECT 19 21
|
| 40 |
+
CONECT 21 19 23 22
|
| 41 |
+
CONECT 22 21
|
| 42 |
+
CONECT 23 24 25 26 21
|
| 43 |
+
CONECT 24 23
|
| 44 |
+
CONECT 25 23
|
| 45 |
+
CONECT 26 23
|
| 46 |
+
END
|
grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/init_structures/gly_gly_grid_0006_0.pdb
ADDED
|
@@ -0,0 +1,46 @@
|
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|
|
|
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|
|
|
|
|
|
|
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|
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|
|
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|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
REMARK 1 CREATED WITH MDTraj 1.10.3, 2026-03-03
|
| 2 |
+
CRYST1 21.749 21.749 21.749 90.00 90.00 90.00 P 1 1
|
| 3 |
+
MODEL 0
|
| 4 |
+
ATOM 1 H1 ACE A 1 14.880 1.010 12.460 1.00 0.00 H
|
| 5 |
+
ATOM 2 CH3 ACE A 1 13.980 1.340 12.980 1.00 0.00 C
|
| 6 |
+
ATOM 3 H2 ACE A 1 13.360 1.800 12.210 1.00 0.00 H
|
| 7 |
+
ATOM 4 H3 ACE A 1 14.260 1.960 13.830 1.00 0.00 H
|
| 8 |
+
ATOM 5 C ACE A 1 13.120 0.150 13.400 1.00 0.00 C
|
| 9 |
+
ATOM 6 O ACE A 1 13.380 -0.970 12.960 1.00 0.00 O
|
| 10 |
+
ATOM 7 N GLY A 2 12.070 0.460 14.140 1.00 0.00 N
|
| 11 |
+
ATOM 8 H GLY A 2 11.880 1.450 14.140 1.00 0.00 H
|
| 12 |
+
ATOM 9 CA GLY A 2 10.850 -0.370 14.360 1.00 0.00 C
|
| 13 |
+
ATOM 10 HA2 GLY A 2 10.540 -0.930 13.480 1.00 0.00 H
|
| 14 |
+
ATOM 11 HA3 GLY A 2 10.990 -1.050 15.200 1.00 0.00 H
|
| 15 |
+
ATOM 12 C GLY A 2 9.660 0.530 14.600 1.00 0.00 C
|
| 16 |
+
ATOM 13 O GLY A 2 9.660 1.690 14.180 1.00 0.00 O
|
| 17 |
+
ATOM 14 N GLY A 3 8.600 0.010 15.140 1.00 0.00 N
|
| 18 |
+
ATOM 15 H GLY A 3 8.590 -0.990 15.280 1.00 0.00 H
|
| 19 |
+
ATOM 16 CA GLY A 3 7.470 0.820 15.580 1.00 0.00 C
|
| 20 |
+
ATOM 17 HA2 GLY A 3 7.810 1.750 16.030 1.00 0.00 H
|
| 21 |
+
ATOM 18 HA3 GLY A 3 6.850 1.000 14.700 1.00 0.00 H
|
| 22 |
+
ATOM 19 C GLY A 3 6.690 0.150 16.650 1.00 0.00 C
|
| 23 |
+
ATOM 20 O GLY A 3 6.140 -0.940 16.300 1.00 0.00 O
|
| 24 |
+
ATOM 21 N NME A 4 6.510 0.700 17.870 1.00 0.00 N
|
| 25 |
+
ATOM 22 H NME A 4 7.000 1.540 18.160 1.00 0.00 H
|
| 26 |
+
ATOM 23 C NME A 4 5.680 0.040 18.880 1.00 0.00 C
|
| 27 |
+
ATOM 24 H1 NME A 4 5.740 -1.050 18.780 1.00 0.00 H
|
| 28 |
+
ATOM 25 H2 NME A 4 6.040 0.280 19.890 1.00 0.00 H
|
| 29 |
+
ATOM 26 H3 NME A 4 4.630 0.330 18.970 1.00 0.00 H
|
| 30 |
+
TER 27 NME A 4
|
| 31 |
+
ENDMDL
|
| 32 |
+
CONECT 1 2
|
| 33 |
+
CONECT 2 5 1 3 4
|
| 34 |
+
CONECT 3 2
|
| 35 |
+
CONECT 4 2
|
| 36 |
+
CONECT 5 2 6 7
|
| 37 |
+
CONECT 6 5
|
| 38 |
+
CONECT 7 5
|
| 39 |
+
CONECT 19 21
|
| 40 |
+
CONECT 21 19 23 22
|
| 41 |
+
CONECT 22 21
|
| 42 |
+
CONECT 23 24 25 26 21
|
| 43 |
+
CONECT 24 23
|
| 44 |
+
CONECT 25 23
|
| 45 |
+
CONECT 26 23
|
| 46 |
+
END
|
grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/init_structures/gly_gly_grid_0007_0.pdb
ADDED
|
@@ -0,0 +1,46 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
REMARK 1 CREATED WITH MDTraj 1.10.3, 2026-03-03
|
| 2 |
+
CRYST1 21.882 21.882 21.882 90.00 90.00 90.00 P 1 1
|
| 3 |
+
MODEL 0
|
| 4 |
+
ATOM 1 H1 ACE A 1 14.010 -0.590 21.790 1.00 0.00 H
|
| 5 |
+
ATOM 2 CH3 ACE A 1 13.850 -0.210 20.780 1.00 0.00 C
|
| 6 |
+
ATOM 3 H2 ACE A 1 12.930 -0.710 20.480 1.00 0.00 H
|
| 7 |
+
ATOM 4 H3 ACE A 1 14.670 -0.370 20.080 1.00 0.00 H
|
| 8 |
+
ATOM 5 C ACE A 1 13.470 1.240 20.830 1.00 0.00 C
|
| 9 |
+
ATOM 6 O ACE A 1 12.300 1.610 20.700 1.00 0.00 O
|
| 10 |
+
ATOM 7 N GLY A 2 14.530 2.110 20.880 1.00 0.00 N
|
| 11 |
+
ATOM 8 H GLY A 2 15.440 1.670 20.800 1.00 0.00 H
|
| 12 |
+
ATOM 9 CA GLY A 2 14.490 3.550 21.050 1.00 0.00 C
|
| 13 |
+
ATOM 10 HA2 GLY A 2 13.650 3.840 20.410 1.00 0.00 H
|
| 14 |
+
ATOM 11 HA3 GLY A 2 14.160 3.730 22.070 1.00 0.00 H
|
| 15 |
+
ATOM 12 C GLY A 2 15.790 4.320 20.740 1.00 0.00 C
|
| 16 |
+
ATOM 13 O GLY A 2 16.700 3.720 20.090 1.00 0.00 O
|
| 17 |
+
ATOM 14 N GLY A 3 15.890 5.570 21.260 1.00 0.00 N
|
| 18 |
+
ATOM 15 H GLY A 3 15.120 5.910 21.820 1.00 0.00 H
|
| 19 |
+
ATOM 16 CA GLY A 3 17.170 6.390 21.300 1.00 0.00 C
|
| 20 |
+
ATOM 17 HA2 GLY A 3 18.110 5.870 21.430 1.00 0.00 H
|
| 21 |
+
ATOM 18 HA3 GLY A 3 17.310 6.910 20.360 1.00 0.00 H
|
| 22 |
+
ATOM 19 C GLY A 3 17.190 7.460 22.380 1.00 0.00 C
|
| 23 |
+
ATOM 20 O GLY A 3 16.170 7.840 22.960 1.00 0.00 O
|
| 24 |
+
ATOM 21 N NME A 4 18.330 7.940 22.770 1.00 0.00 N
|
| 25 |
+
ATOM 22 H NME A 4 19.130 7.600 22.250 1.00 0.00 H
|
| 26 |
+
ATOM 23 C NME A 4 18.630 8.990 23.820 1.00 0.00 C
|
| 27 |
+
ATOM 24 H1 NME A 4 18.720 9.960 23.340 1.00 0.00 H
|
| 28 |
+
ATOM 25 H2 NME A 4 17.800 9.000 24.520 1.00 0.00 H
|
| 29 |
+
ATOM 26 H3 NME A 4 19.580 8.990 24.360 1.00 0.00 H
|
| 30 |
+
TER 27 NME A 4
|
| 31 |
+
ENDMDL
|
| 32 |
+
CONECT 1 2
|
| 33 |
+
CONECT 2 5 1 3 4
|
| 34 |
+
CONECT 3 2
|
| 35 |
+
CONECT 4 2
|
| 36 |
+
CONECT 5 2 6 7
|
| 37 |
+
CONECT 6 5
|
| 38 |
+
CONECT 7 5
|
| 39 |
+
CONECT 19 21
|
| 40 |
+
CONECT 21 19 23 22
|
| 41 |
+
CONECT 22 21
|
| 42 |
+
CONECT 23 24 25 26 21
|
| 43 |
+
CONECT 24 23
|
| 44 |
+
CONECT 25 23
|
| 45 |
+
CONECT 26 23
|
| 46 |
+
END
|
grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/init_structures/gly_gly_grid_0008_0.pdb
ADDED
|
@@ -0,0 +1,46 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
REMARK 1 CREATED WITH MDTraj 1.10.3, 2026-03-03
|
| 2 |
+
CRYST1 21.735 21.735 21.735 90.00 90.00 90.00 P 1 1
|
| 3 |
+
MODEL 0
|
| 4 |
+
ATOM 1 H1 ACE A 1 16.120 14.200 15.300 1.00 0.00 H
|
| 5 |
+
ATOM 2 CH3 ACE A 1 16.820 13.370 15.430 1.00 0.00 C
|
| 6 |
+
ATOM 3 H2 ACE A 1 16.440 12.460 15.900 1.00 0.00 H
|
| 7 |
+
ATOM 4 H3 ACE A 1 17.700 13.690 15.990 1.00 0.00 H
|
| 8 |
+
ATOM 5 C ACE A 1 17.130 12.920 13.990 1.00 0.00 C
|
| 9 |
+
ATOM 6 O ACE A 1 16.240 12.660 13.210 1.00 0.00 O
|
| 10 |
+
ATOM 7 N GLY A 2 18.360 12.900 13.630 1.00 0.00 N
|
| 11 |
+
ATOM 8 H GLY A 2 19.040 13.020 14.370 1.00 0.00 H
|
| 12 |
+
ATOM 9 CA GLY A 2 18.800 12.370 12.330 1.00 0.00 C
|
| 13 |
+
ATOM 10 HA2 GLY A 2 18.230 11.500 12.010 1.00 0.00 H
|
| 14 |
+
ATOM 11 HA3 GLY A 2 18.620 13.190 11.640 1.00 0.00 H
|
| 15 |
+
ATOM 12 C GLY A 2 20.240 11.880 12.380 1.00 0.00 C
|
| 16 |
+
ATOM 13 O GLY A 2 20.820 11.480 13.410 1.00 0.00 O
|
| 17 |
+
ATOM 14 N GLY A 3 20.810 11.860 11.210 1.00 0.00 N
|
| 18 |
+
ATOM 15 H GLY A 3 20.210 12.170 10.460 1.00 0.00 H
|
| 19 |
+
ATOM 16 CA GLY A 3 22.180 11.340 10.960 1.00 0.00 C
|
| 20 |
+
ATOM 17 HA2 GLY A 3 22.580 10.870 11.850 1.00 0.00 H
|
| 21 |
+
ATOM 18 HA3 GLY A 3 22.040 10.590 10.170 1.00 0.00 H
|
| 22 |
+
ATOM 19 C GLY A 3 23.270 12.400 10.470 1.00 0.00 C
|
| 23 |
+
ATOM 20 O GLY A 3 22.970 13.580 10.500 1.00 0.00 O
|
| 24 |
+
ATOM 21 N NME A 4 24.340 11.880 9.880 1.00 0.00 N
|
| 25 |
+
ATOM 22 H NME A 4 24.490 10.890 9.890 1.00 0.00 H
|
| 26 |
+
ATOM 23 C NME A 4 25.170 12.720 8.980 1.00 0.00 C
|
| 27 |
+
ATOM 24 H1 NME A 4 24.600 13.540 8.550 1.00 0.00 H
|
| 28 |
+
ATOM 25 H2 NME A 4 26.030 13.140 9.520 1.00 0.00 H
|
| 29 |
+
ATOM 26 H3 NME A 4 25.490 12.150 8.110 1.00 0.00 H
|
| 30 |
+
TER 27 NME A 4
|
| 31 |
+
ENDMDL
|
| 32 |
+
CONECT 1 2
|
| 33 |
+
CONECT 2 5 1 3 4
|
| 34 |
+
CONECT 3 2
|
| 35 |
+
CONECT 4 2
|
| 36 |
+
CONECT 5 2 6 7
|
| 37 |
+
CONECT 6 5
|
| 38 |
+
CONECT 7 5
|
| 39 |
+
CONECT 19 21
|
| 40 |
+
CONECT 21 19 23 22
|
| 41 |
+
CONECT 22 21
|
| 42 |
+
CONECT 23 24 25 26 21
|
| 43 |
+
CONECT 24 23
|
| 44 |
+
CONECT 25 23
|
| 45 |
+
CONECT 26 23
|
| 46 |
+
END
|
grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/init_structures/gly_gly_grid_0011_0.pdb
ADDED
|
@@ -0,0 +1,46 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
REMARK 1 CREATED WITH MDTraj 1.10.3, 2026-03-03
|
| 2 |
+
CRYST1 21.932 21.932 21.932 90.00 90.00 90.00 P 1 1
|
| 3 |
+
MODEL 0
|
| 4 |
+
ATOM 1 H1 ACE A 1 20.390 22.590 9.120 1.00 0.00 H
|
| 5 |
+
ATOM 2 CH3 ACE A 1 20.110 21.750 8.480 1.00 0.00 C
|
| 6 |
+
ATOM 3 H2 ACE A 1 19.370 21.150 9.000 1.00 0.00 H
|
| 7 |
+
ATOM 4 H3 ACE A 1 21.000 21.120 8.430 1.00 0.00 H
|
| 8 |
+
ATOM 5 C ACE A 1 19.570 22.080 7.110 1.00 0.00 C
|
| 9 |
+
ATOM 6 O ACE A 1 19.490 23.260 6.720 1.00 0.00 O
|
| 10 |
+
ATOM 7 N GLY A 2 19.210 21.120 6.350 1.00 0.00 N
|
| 11 |
+
ATOM 8 H GLY A 2 19.510 20.170 6.560 1.00 0.00 H
|
| 12 |
+
ATOM 9 CA GLY A 2 18.700 21.300 4.930 1.00 0.00 C
|
| 13 |
+
ATOM 10 HA2 GLY A 2 18.000 22.130 4.820 1.00 0.00 H
|
| 14 |
+
ATOM 11 HA3 GLY A 2 19.530 21.530 4.250 1.00 0.00 H
|
| 15 |
+
ATOM 12 C GLY A 2 17.960 20.140 4.290 1.00 0.00 C
|
| 16 |
+
ATOM 13 O GLY A 2 17.410 19.250 4.940 1.00 0.00 O
|
| 17 |
+
ATOM 14 N GLY A 3 17.910 20.210 2.950 1.00 0.00 N
|
| 18 |
+
ATOM 15 H GLY A 3 18.570 20.910 2.650 1.00 0.00 H
|
| 19 |
+
ATOM 16 CA GLY A 3 17.010 19.460 2.070 1.00 0.00 C
|
| 20 |
+
ATOM 17 HA2 GLY A 3 16.240 18.910 2.600 1.00 0.00 H
|
| 21 |
+
ATOM 18 HA3 GLY A 3 16.560 20.170 1.370 1.00 0.00 H
|
| 22 |
+
ATOM 19 C GLY A 3 17.650 18.450 1.100 1.00 0.00 C
|
| 23 |
+
ATOM 20 O GLY A 3 16.990 17.500 0.720 1.00 0.00 O
|
| 24 |
+
ATOM 21 N NME A 4 18.950 18.690 0.740 1.00 0.00 N
|
| 25 |
+
ATOM 22 H NME A 4 19.420 19.440 1.220 1.00 0.00 H
|
| 26 |
+
ATOM 23 C NME A 4 19.670 17.850 -0.240 1.00 0.00 C
|
| 27 |
+
ATOM 24 H1 NME A 4 20.290 17.050 0.170 1.00 0.00 H
|
| 28 |
+
ATOM 25 H2 NME A 4 18.940 17.440 -0.940 1.00 0.00 H
|
| 29 |
+
ATOM 26 H3 NME A 4 20.340 18.470 -0.850 1.00 0.00 H
|
| 30 |
+
TER 27 NME A 4
|
| 31 |
+
ENDMDL
|
| 32 |
+
CONECT 1 2
|
| 33 |
+
CONECT 2 5 1 3 4
|
| 34 |
+
CONECT 3 2
|
| 35 |
+
CONECT 4 2
|
| 36 |
+
CONECT 5 2 6 7
|
| 37 |
+
CONECT 6 5
|
| 38 |
+
CONECT 7 5
|
| 39 |
+
CONECT 19 21
|
| 40 |
+
CONECT 21 19 23 22
|
| 41 |
+
CONECT 22 21
|
| 42 |
+
CONECT 23 24 25 26 21
|
| 43 |
+
CONECT 24 23
|
| 44 |
+
CONECT 25 23
|
| 45 |
+
CONECT 26 23
|
| 46 |
+
END
|
grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/init_structures/gly_gly_grid_0015_0.pdb
ADDED
|
@@ -0,0 +1,46 @@
|
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|
|
|
|
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|
|
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|
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|
|
|
|
|
|
|
|
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|
|
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|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
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|
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|
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|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
REMARK 1 CREATED WITH MDTraj 1.10.3, 2026-03-03
|
| 2 |
+
CRYST1 21.623 21.623 21.623 90.00 90.00 90.00 P 1 1
|
| 3 |
+
MODEL 0
|
| 4 |
+
ATOM 1 H1 ACE A 1 18.440 6.730 17.990 1.00 0.00 H
|
| 5 |
+
ATOM 2 CH3 ACE A 1 18.450 7.580 17.310 1.00 0.00 C
|
| 6 |
+
ATOM 3 H2 ACE A 1 17.560 7.470 16.700 1.00 0.00 H
|
| 7 |
+
ATOM 4 H3 ACE A 1 19.320 7.580 16.650 1.00 0.00 H
|
| 8 |
+
ATOM 5 C ACE A 1 18.350 8.890 18.100 1.00 0.00 C
|
| 9 |
+
ATOM 6 O ACE A 1 19.010 8.930 19.130 1.00 0.00 O
|
| 10 |
+
ATOM 7 N GLY A 2 17.710 9.890 17.600 1.00 0.00 N
|
| 11 |
+
ATOM 8 H GLY A 2 17.310 9.830 16.670 1.00 0.00 H
|
| 12 |
+
ATOM 9 CA GLY A 2 17.780 11.220 18.130 1.00 0.00 C
|
| 13 |
+
ATOM 10 HA2 GLY A 2 17.770 11.190 19.220 1.00 0.00 H
|
| 14 |
+
ATOM 11 HA3 GLY A 2 18.700 11.760 17.890 1.00 0.00 H
|
| 15 |
+
ATOM 12 C GLY A 2 16.610 12.110 17.650 1.00 0.00 C
|
| 16 |
+
ATOM 13 O GLY A 2 15.520 11.600 17.290 1.00 0.00 O
|
| 17 |
+
ATOM 14 N GLY A 3 16.850 13.420 17.720 1.00 0.00 N
|
| 18 |
+
ATOM 15 H GLY A 3 17.730 13.770 18.060 1.00 0.00 H
|
| 19 |
+
ATOM 16 CA GLY A 3 15.910 14.490 17.260 1.00 0.00 C
|
| 20 |
+
ATOM 17 HA2 GLY A 3 14.980 14.020 16.930 1.00 0.00 H
|
| 21 |
+
ATOM 18 HA3 GLY A 3 15.710 15.080 18.150 1.00 0.00 H
|
| 22 |
+
ATOM 19 C GLY A 3 16.450 15.370 16.120 1.00 0.00 C
|
| 23 |
+
ATOM 20 O GLY A 3 17.620 15.540 15.890 1.00 0.00 O
|
| 24 |
+
ATOM 21 N NME A 4 15.480 16.000 15.450 1.00 0.00 N
|
| 25 |
+
ATOM 22 H NME A 4 14.560 15.860 15.860 1.00 0.00 H
|
| 26 |
+
ATOM 23 C NME A 4 15.690 16.750 14.240 1.00 0.00 C
|
| 27 |
+
ATOM 24 H1 NME A 4 14.930 16.540 13.490 1.00 0.00 H
|
| 28 |
+
ATOM 25 H2 NME A 4 15.730 17.830 14.340 1.00 0.00 H
|
| 29 |
+
ATOM 26 H3 NME A 4 16.700 16.610 13.850 1.00 0.00 H
|
| 30 |
+
TER 27 NME A 4
|
| 31 |
+
ENDMDL
|
| 32 |
+
CONECT 1 2
|
| 33 |
+
CONECT 2 5 1 3 4
|
| 34 |
+
CONECT 3 2
|
| 35 |
+
CONECT 4 2
|
| 36 |
+
CONECT 5 2 6 7
|
| 37 |
+
CONECT 6 5
|
| 38 |
+
CONECT 7 5
|
| 39 |
+
CONECT 19 21
|
| 40 |
+
CONECT 21 19 23 22
|
| 41 |
+
CONECT 22 21
|
| 42 |
+
CONECT 23 24 25 26 21
|
| 43 |
+
CONECT 24 23
|
| 44 |
+
CONECT 25 23
|
| 45 |
+
CONECT 26 23
|
| 46 |
+
END
|
grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/init_structures/gly_gly_grid_0016_0.pdb
ADDED
|
@@ -0,0 +1,46 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
REMARK 1 CREATED WITH MDTraj 1.10.3, 2026-03-03
|
| 2 |
+
CRYST1 21.902 21.902 21.902 90.00 90.00 90.00 P 1 1
|
| 3 |
+
MODEL 0
|
| 4 |
+
ATOM 1 H1 ACE A 1 5.530 17.730 5.100 1.00 0.00 H
|
| 5 |
+
ATOM 2 CH3 ACE A 1 6.610 17.590 5.170 1.00 0.00 C
|
| 6 |
+
ATOM 3 H2 ACE A 1 7.140 18.220 4.450 1.00 0.00 H
|
| 7 |
+
ATOM 4 H3 ACE A 1 6.900 16.540 5.130 1.00 0.00 H
|
| 8 |
+
ATOM 5 C ACE A 1 6.900 18.080 6.520 1.00 0.00 C
|
| 9 |
+
ATOM 6 O ACE A 1 6.120 18.860 7.170 1.00 0.00 O
|
| 10 |
+
ATOM 7 N GLY A 2 8.050 17.580 7.080 1.00 0.00 N
|
| 11 |
+
ATOM 8 H GLY A 2 8.660 17.160 6.390 1.00 0.00 H
|
| 12 |
+
ATOM 9 CA GLY A 2 8.680 17.920 8.400 1.00 0.00 C
|
| 13 |
+
ATOM 10 HA2 GLY A 2 8.690 18.960 8.720 1.00 0.00 H
|
| 14 |
+
ATOM 11 HA3 GLY A 2 8.140 17.290 9.110 1.00 0.00 H
|
| 15 |
+
ATOM 12 C GLY A 2 10.170 17.550 8.390 1.00 0.00 C
|
| 16 |
+
ATOM 13 O GLY A 2 10.720 17.350 7.300 1.00 0.00 O
|
| 17 |
+
ATOM 14 N GLY A 3 10.810 17.420 9.580 1.00 0.00 N
|
| 18 |
+
ATOM 15 H GLY A 3 10.270 17.570 10.420 1.00 0.00 H
|
| 19 |
+
ATOM 16 CA GLY A 3 12.110 16.770 9.760 1.00 0.00 C
|
| 20 |
+
ATOM 17 HA2 GLY A 3 12.840 17.170 9.060 1.00 0.00 H
|
| 21 |
+
ATOM 18 HA3 GLY A 3 12.470 17.010 10.760 1.00 0.00 H
|
| 22 |
+
ATOM 19 C GLY A 3 11.970 15.240 9.420 1.00 0.00 C
|
| 23 |
+
ATOM 20 O GLY A 3 11.160 14.830 8.560 1.00 0.00 O
|
| 24 |
+
ATOM 21 N NME A 4 12.820 14.410 10.050 1.00 0.00 N
|
| 25 |
+
ATOM 22 H NME A 4 13.470 14.910 10.640 1.00 0.00 H
|
| 26 |
+
ATOM 23 C NME A 4 12.840 12.900 10.090 1.00 0.00 C
|
| 27 |
+
ATOM 24 H1 NME A 4 13.260 12.550 11.030 1.00 0.00 H
|
| 28 |
+
ATOM 25 H2 NME A 4 11.880 12.410 9.910 1.00 0.00 H
|
| 29 |
+
ATOM 26 H3 NME A 4 13.520 12.610 9.290 1.00 0.00 H
|
| 30 |
+
TER 27 NME A 4
|
| 31 |
+
ENDMDL
|
| 32 |
+
CONECT 1 2
|
| 33 |
+
CONECT 2 5 1 3 4
|
| 34 |
+
CONECT 3 2
|
| 35 |
+
CONECT 4 2
|
| 36 |
+
CONECT 5 2 6 7
|
| 37 |
+
CONECT 6 5
|
| 38 |
+
CONECT 7 5
|
| 39 |
+
CONECT 19 21
|
| 40 |
+
CONECT 21 19 23 22
|
| 41 |
+
CONECT 22 21
|
| 42 |
+
CONECT 23 24 25 26 21
|
| 43 |
+
CONECT 24 23
|
| 44 |
+
CONECT 25 23
|
| 45 |
+
CONECT 26 23
|
| 46 |
+
END
|
grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/init_structures/gly_gly_grid_0018_0.pdb
ADDED
|
@@ -0,0 +1,46 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
REMARK 1 CREATED WITH MDTraj 1.10.3, 2026-03-03
|
| 2 |
+
CRYST1 21.939 21.939 21.939 90.00 90.00 90.00 P 1 1
|
| 3 |
+
MODEL 0
|
| 4 |
+
ATOM 1 H1 ACE A 1 8.960 5.830 7.210 1.00 0.00 H
|
| 5 |
+
ATOM 2 CH3 ACE A 1 8.740 5.510 8.230 1.00 0.00 C
|
| 6 |
+
ATOM 3 H2 ACE A 1 9.570 5.910 8.820 1.00 0.00 H
|
| 7 |
+
ATOM 4 H3 ACE A 1 8.670 4.430 8.310 1.00 0.00 H
|
| 8 |
+
ATOM 5 C ACE A 1 7.470 5.990 8.690 1.00 0.00 C
|
| 9 |
+
ATOM 6 O ACE A 1 6.760 5.320 9.420 1.00 0.00 O
|
| 10 |
+
ATOM 7 N GLY A 2 7.110 7.220 8.350 1.00 0.00 N
|
| 11 |
+
ATOM 8 H GLY A 2 7.770 7.740 7.780 1.00 0.00 H
|
| 12 |
+
ATOM 9 CA GLY A 2 6.000 7.960 8.960 1.00 0.00 C
|
| 13 |
+
ATOM 10 HA2 GLY A 2 5.150 7.320 9.210 1.00 0.00 H
|
| 14 |
+
ATOM 11 HA3 GLY A 2 6.430 8.260 9.910 1.00 0.00 H
|
| 15 |
+
ATOM 12 C GLY A 2 5.540 9.230 8.060 1.00 0.00 C
|
| 16 |
+
ATOM 13 O GLY A 2 5.780 9.330 6.850 1.00 0.00 O
|
| 17 |
+
ATOM 14 N GLY A 3 4.920 10.210 8.680 1.00 0.00 N
|
| 18 |
+
ATOM 15 H GLY A 3 4.710 10.050 9.650 1.00 0.00 H
|
| 19 |
+
ATOM 16 CA GLY A 3 4.460 11.440 8.010 1.00 0.00 C
|
| 20 |
+
ATOM 17 HA2 GLY A 3 4.000 11.180 7.050 1.00 0.00 H
|
| 21 |
+
ATOM 18 HA3 GLY A 3 3.900 12.050 8.710 1.00 0.00 H
|
| 22 |
+
ATOM 19 C GLY A 3 5.670 12.330 7.680 1.00 0.00 C
|
| 23 |
+
ATOM 20 O GLY A 3 6.070 12.500 6.500 1.00 0.00 O
|
| 24 |
+
ATOM 21 N NME A 4 6.280 12.820 8.710 1.00 0.00 N
|
| 25 |
+
ATOM 22 H NME A 4 5.860 12.690 9.620 1.00 0.00 H
|
| 26 |
+
ATOM 23 C NME A 4 7.410 13.790 8.770 1.00 0.00 C
|
| 27 |
+
ATOM 24 H1 NME A 4 8.370 13.350 8.500 1.00 0.00 H
|
| 28 |
+
ATOM 25 H2 NME A 4 7.190 14.640 8.110 1.00 0.00 H
|
| 29 |
+
ATOM 26 H3 NME A 4 7.480 14.150 9.790 1.00 0.00 H
|
| 30 |
+
TER 27 NME A 4
|
| 31 |
+
ENDMDL
|
| 32 |
+
CONECT 1 2
|
| 33 |
+
CONECT 2 5 1 3 4
|
| 34 |
+
CONECT 3 2
|
| 35 |
+
CONECT 4 2
|
| 36 |
+
CONECT 5 2 6 7
|
| 37 |
+
CONECT 6 5
|
| 38 |
+
CONECT 7 5
|
| 39 |
+
CONECT 19 21
|
| 40 |
+
CONECT 21 19 23 22
|
| 41 |
+
CONECT 22 21
|
| 42 |
+
CONECT 23 24 25 26 21
|
| 43 |
+
CONECT 24 23
|
| 44 |
+
CONECT 25 23
|
| 45 |
+
CONECT 26 23
|
| 46 |
+
END
|
grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/init_structures/gly_gly_grid_0019_0.pdb
ADDED
|
@@ -0,0 +1,46 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
REMARK 1 CREATED WITH MDTraj 1.10.3, 2026-03-03
|
| 2 |
+
CRYST1 21.828 21.828 21.828 90.00 90.00 90.00 P 1 1
|
| 3 |
+
MODEL 0
|
| 4 |
+
ATOM 1 H1 ACE A 1 15.870 11.060 -4.300 1.00 0.00 H
|
| 5 |
+
ATOM 2 CH3 ACE A 1 16.690 10.430 -3.960 1.00 0.00 C
|
| 6 |
+
ATOM 3 H2 ACE A 1 17.470 11.140 -3.660 1.00 0.00 H
|
| 7 |
+
ATOM 4 H3 ACE A 1 17.090 9.680 -4.640 1.00 0.00 H
|
| 8 |
+
ATOM 5 C ACE A 1 16.160 9.750 -2.790 1.00 0.00 C
|
| 9 |
+
ATOM 6 O ACE A 1 15.830 8.590 -2.870 1.00 0.00 O
|
| 10 |
+
ATOM 7 N GLY A 2 16.020 10.290 -1.550 1.00 0.00 N
|
| 11 |
+
ATOM 8 H GLY A 2 16.410 11.210 -1.450 1.00 0.00 H
|
| 12 |
+
ATOM 9 CA GLY A 2 15.360 9.640 -0.430 1.00 0.00 C
|
| 13 |
+
ATOM 10 HA2 GLY A 2 14.650 8.950 -0.900 1.00 0.00 H
|
| 14 |
+
ATOM 11 HA3 GLY A 2 16.160 9.080 0.060 1.00 0.00 H
|
| 15 |
+
ATOM 12 C GLY A 2 14.780 10.630 0.600 1.00 0.00 C
|
| 16 |
+
ATOM 13 O GLY A 2 14.470 11.770 0.300 1.00 0.00 O
|
| 17 |
+
ATOM 14 N GLY A 3 14.550 10.200 1.820 1.00 0.00 N
|
| 18 |
+
ATOM 15 H GLY A 3 14.550 9.200 1.980 1.00 0.00 H
|
| 19 |
+
ATOM 16 CA GLY A 3 14.090 11.030 2.940 1.00 0.00 C
|
| 20 |
+
ATOM 17 HA2 GLY A 3 13.200 11.620 2.710 1.00 0.00 H
|
| 21 |
+
ATOM 18 HA3 GLY A 3 13.780 10.330 3.710 1.00 0.00 H
|
| 22 |
+
ATOM 19 C GLY A 3 15.180 11.940 3.500 1.00 0.00 C
|
| 23 |
+
ATOM 20 O GLY A 3 14.830 12.800 4.270 1.00 0.00 O
|
| 24 |
+
ATOM 21 N NME A 4 16.470 11.610 3.250 1.00 0.00 N
|
| 25 |
+
ATOM 22 H NME A 4 16.670 10.820 2.640 1.00 0.00 H
|
| 26 |
+
ATOM 23 C NME A 4 17.600 12.310 3.860 1.00 0.00 C
|
| 27 |
+
ATOM 24 H1 NME A 4 18.500 11.740 3.610 1.00 0.00 H
|
| 28 |
+
ATOM 25 H2 NME A 4 17.840 13.210 3.290 1.00 0.00 H
|
| 29 |
+
ATOM 26 H3 NME A 4 17.410 12.420 4.930 1.00 0.00 H
|
| 30 |
+
TER 27 NME A 4
|
| 31 |
+
ENDMDL
|
| 32 |
+
CONECT 1 2
|
| 33 |
+
CONECT 2 5 1 3 4
|
| 34 |
+
CONECT 3 2
|
| 35 |
+
CONECT 4 2
|
| 36 |
+
CONECT 5 2 6 7
|
| 37 |
+
CONECT 6 5
|
| 38 |
+
CONECT 7 5
|
| 39 |
+
CONECT 19 21
|
| 40 |
+
CONECT 21 19 23 22
|
| 41 |
+
CONECT 22 21
|
| 42 |
+
CONECT 23 24 25 26 21
|
| 43 |
+
CONECT 24 23
|
| 44 |
+
CONECT 25 23
|
| 45 |
+
CONECT 26 23
|
| 46 |
+
END
|
grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/init_structures/gly_gly_grid_0020_0.pdb
ADDED
|
@@ -0,0 +1,46 @@
|
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|
| 1 |
+
REMARK 1 CREATED WITH MDTraj 1.10.3, 2026-03-03
|
| 2 |
+
CRYST1 21.978 21.978 21.978 90.00 90.00 90.00 P 1 1
|
| 3 |
+
MODEL 0
|
| 4 |
+
ATOM 1 H1 ACE A 1 1.960 21.030 7.180 1.00 0.00 H
|
| 5 |
+
ATOM 2 CH3 ACE A 1 2.780 21.700 6.950 1.00 0.00 C
|
| 6 |
+
ATOM 3 H2 ACE A 1 3.110 22.160 7.890 1.00 0.00 H
|
| 7 |
+
ATOM 4 H3 ACE A 1 2.390 22.500 6.310 1.00 0.00 H
|
| 8 |
+
ATOM 5 C ACE A 1 3.980 21.080 6.180 1.00 0.00 C
|
| 9 |
+
ATOM 6 O ACE A 1 5.000 21.730 6.200 1.00 0.00 O
|
| 10 |
+
ATOM 7 N GLY A 2 3.840 19.950 5.570 1.00 0.00 N
|
| 11 |
+
ATOM 8 H GLY A 2 2.930 19.530 5.540 1.00 0.00 H
|
| 12 |
+
ATOM 9 CA GLY A 2 4.790 19.320 4.680 1.00 0.00 C
|
| 13 |
+
ATOM 10 HA2 GLY A 2 5.130 19.970 3.880 1.00 0.00 H
|
| 14 |
+
ATOM 11 HA3 GLY A 2 5.670 19.000 5.240 1.00 0.00 H
|
| 15 |
+
ATOM 12 C GLY A 2 4.120 18.210 3.890 1.00 0.00 C
|
| 16 |
+
ATOM 13 O GLY A 2 2.910 18.230 3.740 1.00 0.00 O
|
| 17 |
+
ATOM 14 N GLY A 3 4.920 17.290 3.350 1.00 0.00 N
|
| 18 |
+
ATOM 15 H GLY A 3 5.920 17.440 3.430 1.00 0.00 H
|
| 19 |
+
ATOM 16 CA GLY A 3 4.580 16.130 2.480 1.00 0.00 C
|
| 20 |
+
ATOM 17 HA2 GLY A 3 4.060 16.520 1.610 1.00 0.00 H
|
| 21 |
+
ATOM 18 HA3 GLY A 3 5.510 15.740 2.080 1.00 0.00 H
|
| 22 |
+
ATOM 19 C GLY A 3 3.770 15.020 2.990 1.00 0.00 C
|
| 23 |
+
ATOM 20 O GLY A 3 3.980 13.840 2.730 1.00 0.00 O
|
| 24 |
+
ATOM 21 N NME A 4 2.900 15.340 3.990 1.00 0.00 N
|
| 25 |
+
ATOM 22 H NME A 4 2.830 16.340 4.110 1.00 0.00 H
|
| 26 |
+
ATOM 23 C NME A 4 1.990 14.530 4.760 1.00 0.00 C
|
| 27 |
+
ATOM 24 H1 NME A 4 1.300 15.240 5.210 1.00 0.00 H
|
| 28 |
+
ATOM 25 H2 NME A 4 1.440 13.910 4.050 1.00 0.00 H
|
| 29 |
+
ATOM 26 H3 NME A 4 2.580 13.930 5.460 1.00 0.00 H
|
| 30 |
+
TER 27 NME A 4
|
| 31 |
+
ENDMDL
|
| 32 |
+
CONECT 1 2
|
| 33 |
+
CONECT 2 5 1 3 4
|
| 34 |
+
CONECT 3 2
|
| 35 |
+
CONECT 4 2
|
| 36 |
+
CONECT 5 2 6 7
|
| 37 |
+
CONECT 6 5
|
| 38 |
+
CONECT 7 5
|
| 39 |
+
CONECT 19 21
|
| 40 |
+
CONECT 21 19 23 22
|
| 41 |
+
CONECT 22 21
|
| 42 |
+
CONECT 23 24 25 26 21
|
| 43 |
+
CONECT 24 23
|
| 44 |
+
CONECT 25 23
|
| 45 |
+
CONECT 26 23
|
| 46 |
+
END
|
grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/init_structures/gly_gly_grid_0041_0.pdb
ADDED
|
@@ -0,0 +1,46 @@
|
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|
|
|
|
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|
|
|
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|
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|
|
|
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|
|
|
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|
|
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|
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|
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|
|
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|
|
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|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
REMARK 1 CREATED WITH MDTraj 1.10.3, 2026-03-03
|
| 2 |
+
CRYST1 21.818 21.818 21.818 90.00 90.00 90.00 P 1 1
|
| 3 |
+
MODEL 0
|
| 4 |
+
ATOM 1 H1 ACE A 1 -2.440 6.450 11.660 1.00 0.00 H
|
| 5 |
+
ATOM 2 CH3 ACE A 1 -2.560 5.960 10.700 1.00 0.00 C
|
| 6 |
+
ATOM 3 H2 ACE A 1 -3.610 6.000 10.430 1.00 0.00 H
|
| 7 |
+
ATOM 4 H3 ACE A 1 -2.310 4.900 10.800 1.00 0.00 H
|
| 8 |
+
ATOM 5 C ACE A 1 -1.660 6.600 9.640 1.00 0.00 C
|
| 9 |
+
ATOM 6 O ACE A 1 -1.370 6.010 8.620 1.00 0.00 O
|
| 10 |
+
ATOM 7 N GLY A 2 -1.170 7.850 9.900 1.00 0.00 N
|
| 11 |
+
ATOM 8 H GLY A 2 -1.420 8.370 10.730 1.00 0.00 H
|
| 12 |
+
ATOM 9 CA GLY A 2 -0.520 8.540 8.840 1.00 0.00 C
|
| 13 |
+
ATOM 10 HA2 GLY A 2 0.080 7.830 8.260 1.00 0.00 H
|
| 14 |
+
ATOM 11 HA3 GLY A 2 -1.300 8.990 8.220 1.00 0.00 H
|
| 15 |
+
ATOM 12 C GLY A 2 0.460 9.620 9.290 1.00 0.00 C
|
| 16 |
+
ATOM 13 O GLY A 2 1.100 9.540 10.350 1.00 0.00 O
|
| 17 |
+
ATOM 14 N GLY A 3 0.690 10.570 8.450 1.00 0.00 N
|
| 18 |
+
ATOM 15 H GLY A 3 0.080 10.670 7.650 1.00 0.00 H
|
| 19 |
+
ATOM 16 CA GLY A 3 1.510 11.750 8.690 1.00 0.00 C
|
| 20 |
+
ATOM 17 HA2 GLY A 3 1.510 12.460 7.860 1.00 0.00 H
|
| 21 |
+
ATOM 18 HA3 GLY A 3 1.060 12.100 9.620 1.00 0.00 H
|
| 22 |
+
ATOM 19 C GLY A 3 2.960 11.420 8.850 1.00 0.00 C
|
| 23 |
+
ATOM 20 O GLY A 3 3.600 10.900 7.900 1.00 0.00 O
|
| 24 |
+
ATOM 21 N NME A 4 3.620 11.660 9.970 1.00 0.00 N
|
| 25 |
+
ATOM 22 H NME A 4 3.160 12.230 10.670 1.00 0.00 H
|
| 26 |
+
ATOM 23 C NME A 4 5.080 11.530 10.170 1.00 0.00 C
|
| 27 |
+
ATOM 24 H1 NME A 4 5.570 12.500 10.030 1.00 0.00 H
|
| 28 |
+
ATOM 25 H2 NME A 4 5.270 11.180 11.180 1.00 0.00 H
|
| 29 |
+
ATOM 26 H3 NME A 4 5.490 10.820 9.460 1.00 0.00 H
|
| 30 |
+
TER 27 NME A 4
|
| 31 |
+
ENDMDL
|
| 32 |
+
CONECT 1 2
|
| 33 |
+
CONECT 2 5 1 3 4
|
| 34 |
+
CONECT 3 2
|
| 35 |
+
CONECT 4 2
|
| 36 |
+
CONECT 5 2 6 7
|
| 37 |
+
CONECT 6 5
|
| 38 |
+
CONECT 7 5
|
| 39 |
+
CONECT 19 21
|
| 40 |
+
CONECT 21 19 23 22
|
| 41 |
+
CONECT 22 21
|
| 42 |
+
CONECT 23 24 25 26 21
|
| 43 |
+
CONECT 24 23
|
| 44 |
+
CONECT 25 23
|
| 45 |
+
CONECT 26 23
|
| 46 |
+
END
|
grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/init_structures/gly_gly_grid_0042_0.pdb
ADDED
|
@@ -0,0 +1,46 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
REMARK 1 CREATED WITH MDTraj 1.10.3, 2026-03-03
|
| 2 |
+
CRYST1 21.845 21.845 21.845 90.00 90.00 90.00 P 1 1
|
| 3 |
+
MODEL 0
|
| 4 |
+
ATOM 1 H1 ACE A 1 21.010 -4.260 15.680 1.00 0.00 H
|
| 5 |
+
ATOM 2 CH3 ACE A 1 20.590 -3.490 15.040 1.00 0.00 C
|
| 6 |
+
ATOM 3 H2 ACE A 1 19.770 -2.960 15.530 1.00 0.00 H
|
| 7 |
+
ATOM 4 H3 ACE A 1 20.310 -4.050 14.160 1.00 0.00 H
|
| 8 |
+
ATOM 5 C ACE A 1 21.680 -2.560 14.740 1.00 0.00 C
|
| 9 |
+
ATOM 6 O ACE A 1 22.840 -2.760 15.120 1.00 0.00 O
|
| 10 |
+
ATOM 7 N GLY A 2 21.250 -1.440 14.150 1.00 0.00 N
|
| 11 |
+
ATOM 8 H GLY A 2 20.320 -1.570 13.780 1.00 0.00 H
|
| 12 |
+
ATOM 9 CA GLY A 2 22.090 -0.350 13.560 1.00 0.00 C
|
| 13 |
+
ATOM 10 HA2 GLY A 2 22.920 -0.270 14.260 1.00 0.00 H
|
| 14 |
+
ATOM 11 HA3 GLY A 2 22.440 -0.640 12.570 1.00 0.00 H
|
| 15 |
+
ATOM 12 C GLY A 2 21.340 0.970 13.470 1.00 0.00 C
|
| 16 |
+
ATOM 13 O GLY A 2 20.270 1.270 14.080 1.00 0.00 O
|
| 17 |
+
ATOM 14 N GLY A 3 21.810 1.920 12.590 1.00 0.00 N
|
| 18 |
+
ATOM 15 H GLY A 3 22.710 1.720 12.190 1.00 0.00 H
|
| 19 |
+
ATOM 16 CA GLY A 3 21.170 3.150 12.120 1.00 0.00 C
|
| 20 |
+
ATOM 17 HA2 GLY A 3 21.750 3.420 11.230 1.00 0.00 H
|
| 21 |
+
ATOM 18 HA3 GLY A 3 20.180 2.910 11.740 1.00 0.00 H
|
| 22 |
+
ATOM 19 C GLY A 3 21.020 4.410 13.000 1.00 0.00 C
|
| 23 |
+
ATOM 20 O GLY A 3 21.520 5.510 12.730 1.00 0.00 O
|
| 24 |
+
ATOM 21 N NME A 4 20.270 4.190 14.110 1.00 0.00 N
|
| 25 |
+
ATOM 22 H NME A 4 19.950 3.240 14.210 1.00 0.00 H
|
| 26 |
+
ATOM 23 C NME A 4 20.050 5.200 15.170 1.00 0.00 C
|
| 27 |
+
ATOM 24 H1 NME A 4 20.970 5.280 15.740 1.00 0.00 H
|
| 28 |
+
ATOM 25 H2 NME A 4 19.770 6.100 14.630 1.00 0.00 H
|
| 29 |
+
ATOM 26 H3 NME A 4 19.200 4.880 15.770 1.00 0.00 H
|
| 30 |
+
TER 27 NME A 4
|
| 31 |
+
ENDMDL
|
| 32 |
+
CONECT 1 2
|
| 33 |
+
CONECT 2 5 1 3 4
|
| 34 |
+
CONECT 3 2
|
| 35 |
+
CONECT 4 2
|
| 36 |
+
CONECT 5 2 6 7
|
| 37 |
+
CONECT 6 5
|
| 38 |
+
CONECT 7 5
|
| 39 |
+
CONECT 19 21
|
| 40 |
+
CONECT 21 19 23 22
|
| 41 |
+
CONECT 22 21
|
| 42 |
+
CONECT 23 24 25 26 21
|
| 43 |
+
CONECT 24 23
|
| 44 |
+
CONECT 25 23
|
| 45 |
+
CONECT 26 23
|
| 46 |
+
END
|
grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/init_structures/gly_gly_grid_0046_0.pdb
ADDED
|
@@ -0,0 +1,46 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
REMARK 1 CREATED WITH MDTraj 1.10.3, 2026-03-03
|
| 2 |
+
CRYST1 21.690 21.690 21.690 90.00 90.00 90.00 P 1 1
|
| 3 |
+
MODEL 0
|
| 4 |
+
ATOM 1 H1 ACE A 1 18.230 3.290 10.600 1.00 0.00 H
|
| 5 |
+
ATOM 2 CH3 ACE A 1 17.790 4.200 11.020 1.00 0.00 C
|
| 6 |
+
ATOM 3 H2 ACE A 1 16.990 3.940 11.710 1.00 0.00 H
|
| 7 |
+
ATOM 4 H3 ACE A 1 17.440 4.790 10.170 1.00 0.00 H
|
| 8 |
+
ATOM 5 C ACE A 1 18.720 4.870 12.010 1.00 0.00 C
|
| 9 |
+
ATOM 6 O ACE A 1 19.440 4.200 12.710 1.00 0.00 O
|
| 10 |
+
ATOM 7 N GLY A 2 18.800 6.240 11.940 1.00 0.00 N
|
| 11 |
+
ATOM 8 H GLY A 2 18.070 6.670 11.380 1.00 0.00 H
|
| 12 |
+
ATOM 9 CA GLY A 2 19.650 7.070 12.810 1.00 0.00 C
|
| 13 |
+
ATOM 10 HA2 GLY A 2 19.660 6.640 13.810 1.00 0.00 H
|
| 14 |
+
ATOM 11 HA3 GLY A 2 20.680 7.070 12.460 1.00 0.00 H
|
| 15 |
+
ATOM 12 C GLY A 2 19.150 8.480 12.990 1.00 0.00 C
|
| 16 |
+
ATOM 13 O GLY A 2 17.920 8.750 12.720 1.00 0.00 O
|
| 17 |
+
ATOM 14 N GLY A 3 20.060 9.400 13.430 1.00 0.00 N
|
| 18 |
+
ATOM 15 H GLY A 3 21.050 9.180 13.460 1.00 0.00 H
|
| 19 |
+
ATOM 16 CA GLY A 3 19.750 10.830 13.680 1.00 0.00 C
|
| 20 |
+
ATOM 17 HA2 GLY A 3 20.620 11.350 14.060 1.00 0.00 H
|
| 21 |
+
ATOM 18 HA3 GLY A 3 19.400 11.310 12.760 1.00 0.00 H
|
| 22 |
+
ATOM 19 C GLY A 3 18.610 11.010 14.710 1.00 0.00 C
|
| 23 |
+
ATOM 20 O GLY A 3 17.430 10.730 14.490 1.00 0.00 O
|
| 24 |
+
ATOM 21 N NME A 4 18.970 11.610 15.880 1.00 0.00 N
|
| 25 |
+
ATOM 22 H NME A 4 19.910 11.980 16.000 1.00 0.00 H
|
| 26 |
+
ATOM 23 C NME A 4 18.050 11.980 16.920 1.00 0.00 C
|
| 27 |
+
ATOM 24 H1 NME A 4 18.100 11.280 17.750 1.00 0.00 H
|
| 28 |
+
ATOM 25 H2 NME A 4 18.490 12.840 17.440 1.00 0.00 H
|
| 29 |
+
ATOM 26 H3 NME A 4 17.010 12.080 16.630 1.00 0.00 H
|
| 30 |
+
TER 27 NME A 4
|
| 31 |
+
ENDMDL
|
| 32 |
+
CONECT 1 2
|
| 33 |
+
CONECT 2 5 1 3 4
|
| 34 |
+
CONECT 3 2
|
| 35 |
+
CONECT 4 2
|
| 36 |
+
CONECT 5 2 6 7
|
| 37 |
+
CONECT 6 5
|
| 38 |
+
CONECT 7 5
|
| 39 |
+
CONECT 19 21
|
| 40 |
+
CONECT 21 19 23 22
|
| 41 |
+
CONECT 22 21
|
| 42 |
+
CONECT 23 24 25 26 21
|
| 43 |
+
CONECT 24 23
|
| 44 |
+
CONECT 25 23
|
| 45 |
+
CONECT 26 23
|
| 46 |
+
END
|
grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/init_structures/gly_gly_grid_0047_0.pdb
ADDED
|
@@ -0,0 +1,46 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
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|
|
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|
|
|
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|
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|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
REMARK 1 CREATED WITH MDTraj 1.10.3, 2026-03-03
|
| 2 |
+
CRYST1 21.763 21.763 21.763 90.00 90.00 90.00 P 1 1
|
| 3 |
+
MODEL 0
|
| 4 |
+
ATOM 1 H1 ACE A 1 22.350 6.650 13.050 1.00 0.00 H
|
| 5 |
+
ATOM 2 CH3 ACE A 1 22.000 6.860 14.060 1.00 0.00 C
|
| 6 |
+
ATOM 3 H2 ACE A 1 22.090 7.930 14.220 1.00 0.00 H
|
| 7 |
+
ATOM 4 H3 ACE A 1 22.670 6.380 14.780 1.00 0.00 H
|
| 8 |
+
ATOM 5 C ACE A 1 20.630 6.380 14.170 1.00 0.00 C
|
| 9 |
+
ATOM 6 O ACE A 1 19.770 7.140 14.640 1.00 0.00 O
|
| 10 |
+
ATOM 7 N GLY A 2 20.460 5.180 13.640 1.00 0.00 N
|
| 11 |
+
ATOM 8 H GLY A 2 21.280 4.790 13.210 1.00 0.00 H
|
| 12 |
+
ATOM 9 CA GLY A 2 19.150 4.530 13.300 1.00 0.00 C
|
| 13 |
+
ATOM 10 HA2 GLY A 2 18.420 4.750 14.080 1.00 0.00 H
|
| 14 |
+
ATOM 11 HA3 GLY A 2 18.830 4.960 12.350 1.00 0.00 H
|
| 15 |
+
ATOM 12 C GLY A 2 19.240 3.060 13.140 1.00 0.00 C
|
| 16 |
+
ATOM 13 O GLY A 2 20.290 2.470 13.540 1.00 0.00 O
|
| 17 |
+
ATOM 14 N GLY A 3 18.270 2.460 12.500 1.00 0.00 N
|
| 18 |
+
ATOM 15 H GLY A 3 17.540 3.050 12.140 1.00 0.00 H
|
| 19 |
+
ATOM 16 CA GLY A 3 18.170 1.010 12.300 1.00 0.00 C
|
| 20 |
+
ATOM 17 HA2 GLY A 3 17.480 0.800 11.480 1.00 0.00 H
|
| 21 |
+
ATOM 18 HA3 GLY A 3 19.100 0.680 11.850 1.00 0.00 H
|
| 22 |
+
ATOM 19 C GLY A 3 17.910 0.220 13.600 1.00 0.00 C
|
| 23 |
+
ATOM 20 O GLY A 3 18.050 0.820 14.700 1.00 0.00 O
|
| 24 |
+
ATOM 21 N NME A 4 17.380 -1.020 13.430 1.00 0.00 N
|
| 25 |
+
ATOM 22 H NME A 4 17.180 -1.400 12.510 1.00 0.00 H
|
| 26 |
+
ATOM 23 C NME A 4 17.350 -1.990 14.540 1.00 0.00 C
|
| 27 |
+
ATOM 24 H1 NME A 4 17.230 -1.550 15.530 1.00 0.00 H
|
| 28 |
+
ATOM 25 H2 NME A 4 16.510 -2.680 14.430 1.00 0.00 H
|
| 29 |
+
ATOM 26 H3 NME A 4 18.300 -2.530 14.560 1.00 0.00 H
|
| 30 |
+
TER 27 NME A 4
|
| 31 |
+
ENDMDL
|
| 32 |
+
CONECT 1 2
|
| 33 |
+
CONECT 2 5 1 3 4
|
| 34 |
+
CONECT 3 2
|
| 35 |
+
CONECT 4 2
|
| 36 |
+
CONECT 5 2 6 7
|
| 37 |
+
CONECT 6 5
|
| 38 |
+
CONECT 7 5
|
| 39 |
+
CONECT 19 21
|
| 40 |
+
CONECT 21 19 23 22
|
| 41 |
+
CONECT 22 21
|
| 42 |
+
CONECT 23 24 25 26 21
|
| 43 |
+
CONECT 24 23
|
| 44 |
+
CONECT 25 23
|
| 45 |
+
CONECT 26 23
|
| 46 |
+
END
|
grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/init_structures/gly_gly_grid_0048_0.pdb
ADDED
|
@@ -0,0 +1,46 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
REMARK 1 CREATED WITH MDTraj 1.10.3, 2026-03-03
|
| 2 |
+
CRYST1 21.794 21.794 21.794 90.00 90.00 90.00 P 1 1
|
| 3 |
+
MODEL 0
|
| 4 |
+
ATOM 1 H1 ACE A 1 19.160 6.170 2.270 1.00 0.00 H
|
| 5 |
+
ATOM 2 CH3 ACE A 1 19.130 5.210 2.770 1.00 0.00 C
|
| 6 |
+
ATOM 3 H2 ACE A 1 19.630 5.210 3.740 1.00 0.00 H
|
| 7 |
+
ATOM 4 H3 ACE A 1 19.450 4.420 2.090 1.00 0.00 H
|
| 8 |
+
ATOM 5 C ACE A 1 17.640 4.880 2.940 1.00 0.00 C
|
| 9 |
+
ATOM 6 O ACE A 1 17.130 4.150 2.130 1.00 0.00 O
|
| 10 |
+
ATOM 7 N GLY A 2 16.980 5.450 3.910 1.00 0.00 N
|
| 11 |
+
ATOM 8 H GLY A 2 17.370 6.330 4.210 1.00 0.00 H
|
| 12 |
+
ATOM 9 CA GLY A 2 15.590 5.180 4.200 1.00 0.00 C
|
| 13 |
+
ATOM 10 HA2 GLY A 2 15.100 4.970 3.250 1.00 0.00 H
|
| 14 |
+
ATOM 11 HA3 GLY A 2 15.600 4.270 4.810 1.00 0.00 H
|
| 15 |
+
ATOM 12 C GLY A 2 14.940 6.350 4.950 1.00 0.00 C
|
| 16 |
+
ATOM 13 O GLY A 2 15.470 7.460 5.060 1.00 0.00 O
|
| 17 |
+
ATOM 14 N GLY A 3 13.880 6.070 5.650 1.00 0.00 N
|
| 18 |
+
ATOM 15 H GLY A 3 13.590 5.100 5.670 1.00 0.00 H
|
| 19 |
+
ATOM 16 CA GLY A 3 13.000 6.880 6.450 1.00 0.00 C
|
| 20 |
+
ATOM 17 HA2 GLY A 3 12.930 6.450 7.450 1.00 0.00 H
|
| 21 |
+
ATOM 18 HA3 GLY A 3 13.400 7.890 6.440 1.00 0.00 H
|
| 22 |
+
ATOM 19 C GLY A 3 11.600 6.970 5.900 1.00 0.00 C
|
| 23 |
+
ATOM 20 O GLY A 3 11.060 6.070 5.240 1.00 0.00 O
|
| 24 |
+
ATOM 21 N NME A 4 10.960 8.000 6.410 1.00 0.00 N
|
| 25 |
+
ATOM 22 H NME A 4 11.500 8.670 6.930 1.00 0.00 H
|
| 26 |
+
ATOM 23 C NME A 4 9.570 8.310 5.990 1.00 0.00 C
|
| 27 |
+
ATOM 24 H1 NME A 4 8.860 7.490 6.150 1.00 0.00 H
|
| 28 |
+
ATOM 25 H2 NME A 4 9.090 9.200 6.390 1.00 0.00 H
|
| 29 |
+
ATOM 26 H3 NME A 4 9.670 8.500 4.920 1.00 0.00 H
|
| 30 |
+
TER 27 NME A 4
|
| 31 |
+
ENDMDL
|
| 32 |
+
CONECT 1 2
|
| 33 |
+
CONECT 2 5 1 3 4
|
| 34 |
+
CONECT 3 2
|
| 35 |
+
CONECT 4 2
|
| 36 |
+
CONECT 5 2 6 7
|
| 37 |
+
CONECT 6 5
|
| 38 |
+
CONECT 7 5
|
| 39 |
+
CONECT 19 21
|
| 40 |
+
CONECT 21 19 23 22
|
| 41 |
+
CONECT 22 21
|
| 42 |
+
CONECT 23 24 25 26 21
|
| 43 |
+
CONECT 24 23
|
| 44 |
+
CONECT 25 23
|
| 45 |
+
CONECT 26 23
|
| 46 |
+
END
|
grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/init_structures/gly_gly_grid_0052_0.pdb
ADDED
|
@@ -0,0 +1,46 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
REMARK 1 CREATED WITH MDTraj 1.10.3, 2026-03-03
|
| 2 |
+
CRYST1 21.891 21.891 21.891 90.00 90.00 90.00 P 1 1
|
| 3 |
+
MODEL 0
|
| 4 |
+
ATOM 1 H1 ACE A 1 21.180 11.730 21.780 1.00 0.00 H
|
| 5 |
+
ATOM 2 CH3 ACE A 1 20.930 12.020 20.760 1.00 0.00 C
|
| 6 |
+
ATOM 3 H2 ACE A 1 21.460 11.350 20.080 1.00 0.00 H
|
| 7 |
+
ATOM 4 H3 ACE A 1 21.180 13.030 20.450 1.00 0.00 H
|
| 8 |
+
ATOM 5 C ACE A 1 19.480 11.750 20.510 1.00 0.00 C
|
| 9 |
+
ATOM 6 O ACE A 1 19.160 11.260 19.440 1.00 0.00 O
|
| 10 |
+
ATOM 7 N GLY A 2 18.650 12.170 21.470 1.00 0.00 N
|
| 11 |
+
ATOM 8 H GLY A 2 19.010 12.500 22.350 1.00 0.00 H
|
| 12 |
+
ATOM 9 CA GLY A 2 17.210 12.280 21.300 1.00 0.00 C
|
| 13 |
+
ATOM 10 HA2 GLY A 2 17.070 12.670 20.290 1.00 0.00 H
|
| 14 |
+
ATOM 11 HA3 GLY A 2 16.710 11.320 21.380 1.00 0.00 H
|
| 15 |
+
ATOM 12 C GLY A 2 16.470 13.300 22.240 1.00 0.00 C
|
| 16 |
+
ATOM 13 O GLY A 2 17.050 14.250 22.730 1.00 0.00 O
|
| 17 |
+
ATOM 14 N GLY A 3 15.190 13.010 22.470 1.00 0.00 N
|
| 18 |
+
ATOM 15 H GLY A 3 14.930 12.110 22.110 1.00 0.00 H
|
| 19 |
+
ATOM 16 CA GLY A 3 14.380 13.670 23.480 1.00 0.00 C
|
| 20 |
+
ATOM 17 HA2 GLY A 3 13.990 12.940 24.190 1.00 0.00 H
|
| 21 |
+
ATOM 18 HA3 GLY A 3 14.990 14.400 24.020 1.00 0.00 H
|
| 22 |
+
ATOM 19 C GLY A 3 13.220 14.570 23.000 1.00 0.00 C
|
| 23 |
+
ATOM 20 O GLY A 3 12.720 15.410 23.710 1.00 0.00 O
|
| 24 |
+
ATOM 21 N NME A 4 12.860 14.340 21.720 1.00 0.00 N
|
| 25 |
+
ATOM 22 H NME A 4 13.410 13.670 21.200 1.00 0.00 H
|
| 26 |
+
ATOM 23 C NME A 4 11.860 15.070 21.040 1.00 0.00 C
|
| 27 |
+
ATOM 24 H1 NME A 4 11.220 14.420 20.440 1.00 0.00 H
|
| 28 |
+
ATOM 25 H2 NME A 4 11.230 15.470 21.840 1.00 0.00 H
|
| 29 |
+
ATOM 26 H3 NME A 4 12.240 15.910 20.450 1.00 0.00 H
|
| 30 |
+
TER 27 NME A 4
|
| 31 |
+
ENDMDL
|
| 32 |
+
CONECT 1 2
|
| 33 |
+
CONECT 2 5 1 3 4
|
| 34 |
+
CONECT 3 2
|
| 35 |
+
CONECT 4 2
|
| 36 |
+
CONECT 5 2 6 7
|
| 37 |
+
CONECT 6 5
|
| 38 |
+
CONECT 7 5
|
| 39 |
+
CONECT 19 21
|
| 40 |
+
CONECT 21 19 23 22
|
| 41 |
+
CONECT 22 21
|
| 42 |
+
CONECT 23 24 25 26 21
|
| 43 |
+
CONECT 24 23
|
| 44 |
+
CONECT 25 23
|
| 45 |
+
CONECT 26 23
|
| 46 |
+
END
|
grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/init_structures/gly_gly_grid_0054_0.pdb
ADDED
|
@@ -0,0 +1,46 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
REMARK 1 CREATED WITH MDTraj 1.10.3, 2026-03-03
|
| 2 |
+
CRYST1 21.878 21.878 21.878 90.00 90.00 90.00 P 1 1
|
| 3 |
+
MODEL 0
|
| 4 |
+
ATOM 1 H1 ACE A 1 1.260 2.990 -0.210 1.00 0.00 H
|
| 5 |
+
ATOM 2 CH3 ACE A 1 1.660 2.490 0.680 1.00 0.00 C
|
| 6 |
+
ATOM 3 H2 ACE A 1 2.010 1.470 0.580 1.00 0.00 H
|
| 7 |
+
ATOM 4 H3 ACE A 1 0.940 2.600 1.490 1.00 0.00 H
|
| 8 |
+
ATOM 5 C ACE A 1 2.900 3.340 1.010 1.00 0.00 C
|
| 9 |
+
ATOM 6 O ACE A 1 2.830 4.490 0.680 1.00 0.00 O
|
| 10 |
+
ATOM 7 N GLY A 2 3.900 2.870 1.680 1.00 0.00 N
|
| 11 |
+
ATOM 8 H GLY A 2 3.950 1.890 1.920 1.00 0.00 H
|
| 12 |
+
ATOM 9 CA GLY A 2 5.200 3.460 1.940 1.00 0.00 C
|
| 13 |
+
ATOM 10 HA2 GLY A 2 5.350 4.100 1.070 1.00 0.00 H
|
| 14 |
+
ATOM 11 HA3 GLY A 2 5.160 4.140 2.790 1.00 0.00 H
|
| 15 |
+
ATOM 12 C GLY A 2 6.260 2.460 2.220 1.00 0.00 C
|
| 16 |
+
ATOM 13 O GLY A 2 6.290 1.310 1.820 1.00 0.00 O
|
| 17 |
+
ATOM 14 N GLY A 3 7.260 2.940 2.990 1.00 0.00 N
|
| 18 |
+
ATOM 15 H GLY A 3 7.280 3.940 3.110 1.00 0.00 H
|
| 19 |
+
ATOM 16 CA GLY A 3 8.390 2.200 3.430 1.00 0.00 C
|
| 20 |
+
ATOM 17 HA2 GLY A 3 8.450 2.290 4.510 1.00 0.00 H
|
| 21 |
+
ATOM 18 HA3 GLY A 3 8.310 1.160 3.100 1.00 0.00 H
|
| 22 |
+
ATOM 19 C GLY A 3 9.610 2.770 2.770 1.00 0.00 C
|
| 23 |
+
ATOM 20 O GLY A 3 9.550 2.790 1.530 1.00 0.00 O
|
| 24 |
+
ATOM 21 N NME A 4 10.610 3.160 3.570 1.00 0.00 N
|
| 25 |
+
ATOM 22 H NME A 4 10.490 3.050 4.570 1.00 0.00 H
|
| 26 |
+
ATOM 23 C NME A 4 11.710 4.110 3.150 1.00 0.00 C
|
| 27 |
+
ATOM 24 H1 NME A 4 11.280 5.020 2.730 1.00 0.00 H
|
| 28 |
+
ATOM 25 H2 NME A 4 12.220 4.340 4.090 1.00 0.00 H
|
| 29 |
+
ATOM 26 H3 NME A 4 12.380 3.600 2.460 1.00 0.00 H
|
| 30 |
+
TER 27 NME A 4
|
| 31 |
+
ENDMDL
|
| 32 |
+
CONECT 1 2
|
| 33 |
+
CONECT 2 5 1 3 4
|
| 34 |
+
CONECT 3 2
|
| 35 |
+
CONECT 4 2
|
| 36 |
+
CONECT 5 2 6 7
|
| 37 |
+
CONECT 6 5
|
| 38 |
+
CONECT 7 5
|
| 39 |
+
CONECT 19 21
|
| 40 |
+
CONECT 21 19 23 22
|
| 41 |
+
CONECT 22 21
|
| 42 |
+
CONECT 23 24 25 26 21
|
| 43 |
+
CONECT 24 23
|
| 44 |
+
CONECT 25 23
|
| 45 |
+
CONECT 26 23
|
| 46 |
+
END
|
grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/init_structures/gly_gly_grid_0056_0.pdb
ADDED
|
@@ -0,0 +1,46 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
REMARK 1 CREATED WITH MDTraj 1.10.3, 2026-03-03
|
| 2 |
+
CRYST1 21.898 21.898 21.898 90.00 90.00 90.00 P 1 1
|
| 3 |
+
MODEL 0
|
| 4 |
+
ATOM 1 H1 ACE A 1 3.320 4.710 7.150 1.00 0.00 H
|
| 5 |
+
ATOM 2 CH3 ACE A 1 2.560 5.050 7.850 1.00 0.00 C
|
| 6 |
+
ATOM 3 H2 ACE A 1 2.460 4.380 8.710 1.00 0.00 H
|
| 7 |
+
ATOM 4 H3 ACE A 1 1.650 4.890 7.280 1.00 0.00 H
|
| 8 |
+
ATOM 5 C ACE A 1 2.790 6.430 8.490 1.00 0.00 C
|
| 9 |
+
ATOM 6 O ACE A 1 1.830 7.180 8.790 1.00 0.00 O
|
| 10 |
+
ATOM 7 N GLY A 2 4.050 6.670 8.960 1.00 0.00 N
|
| 11 |
+
ATOM 8 H GLY A 2 4.700 5.900 8.830 1.00 0.00 H
|
| 12 |
+
ATOM 9 CA GLY A 2 4.440 7.870 9.760 1.00 0.00 C
|
| 13 |
+
ATOM 10 HA2 GLY A 2 3.840 8.740 9.480 1.00 0.00 H
|
| 14 |
+
ATOM 11 HA3 GLY A 2 4.190 7.710 10.820 1.00 0.00 H
|
| 15 |
+
ATOM 12 C GLY A 2 5.960 8.150 9.650 1.00 0.00 C
|
| 16 |
+
ATOM 13 O GLY A 2 6.480 7.760 8.640 1.00 0.00 O
|
| 17 |
+
ATOM 14 N GLY A 3 6.520 8.910 10.610 1.00 0.00 N
|
| 18 |
+
ATOM 15 H GLY A 3 5.830 9.450 11.110 1.00 0.00 H
|
| 19 |
+
ATOM 16 CA GLY A 3 8.000 9.280 10.630 1.00 0.00 C
|
| 20 |
+
ATOM 17 HA2 GLY A 3 8.620 8.410 10.840 1.00 0.00 H
|
| 21 |
+
ATOM 18 HA3 GLY A 3 8.340 9.530 9.630 1.00 0.00 H
|
| 22 |
+
ATOM 19 C GLY A 3 8.240 10.490 11.520 1.00 0.00 C
|
| 23 |
+
ATOM 20 O GLY A 3 7.480 10.730 12.520 1.00 0.00 O
|
| 24 |
+
ATOM 21 N NME A 4 9.320 11.190 11.290 1.00 0.00 N
|
| 25 |
+
ATOM 22 H NME A 4 9.750 11.030 10.390 1.00 0.00 H
|
| 26 |
+
ATOM 23 C NME A 4 9.900 12.230 12.190 1.00 0.00 C
|
| 27 |
+
ATOM 24 H1 NME A 4 9.280 13.120 12.210 1.00 0.00 H
|
| 28 |
+
ATOM 25 H2 NME A 4 10.140 11.780 13.160 1.00 0.00 H
|
| 29 |
+
ATOM 26 H3 NME A 4 10.860 12.620 11.860 1.00 0.00 H
|
| 30 |
+
TER 27 NME A 4
|
| 31 |
+
ENDMDL
|
| 32 |
+
CONECT 1 2
|
| 33 |
+
CONECT 2 5 1 3 4
|
| 34 |
+
CONECT 3 2
|
| 35 |
+
CONECT 4 2
|
| 36 |
+
CONECT 5 2 6 7
|
| 37 |
+
CONECT 6 5
|
| 38 |
+
CONECT 7 5
|
| 39 |
+
CONECT 19 21
|
| 40 |
+
CONECT 21 19 23 22
|
| 41 |
+
CONECT 22 21
|
| 42 |
+
CONECT 23 24 25 26 21
|
| 43 |
+
CONECT 24 23
|
| 44 |
+
CONECT 25 23
|
| 45 |
+
CONECT 26 23
|
| 46 |
+
END
|
grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/init_structures/gly_gly_grid_0059_0.pdb
ADDED
|
@@ -0,0 +1,46 @@
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
REMARK 1 CREATED WITH MDTraj 1.10.3, 2026-03-03
|
| 2 |
+
CRYST1 21.807 21.807 21.807 90.00 90.00 90.00 P 1 1
|
| 3 |
+
MODEL 0
|
| 4 |
+
ATOM 1 H1 ACE A 1 15.490 7.460 14.540 1.00 0.00 H
|
| 5 |
+
ATOM 2 CH3 ACE A 1 16.560 7.600 14.650 1.00 0.00 C
|
| 6 |
+
ATOM 3 H2 ACE A 1 16.800 8.660 14.710 1.00 0.00 H
|
| 7 |
+
ATOM 4 H3 ACE A 1 16.940 7.210 13.700 1.00 0.00 H
|
| 8 |
+
ATOM 5 C ACE A 1 17.030 6.890 15.890 1.00 0.00 C
|
| 9 |
+
ATOM 6 O ACE A 1 17.770 5.980 15.770 1.00 0.00 O
|
| 10 |
+
ATOM 7 N GLY A 2 16.560 7.310 17.010 1.00 0.00 N
|
| 11 |
+
ATOM 8 H GLY A 2 15.970 8.120 17.100 1.00 0.00 H
|
| 12 |
+
ATOM 9 CA GLY A 2 16.860 6.630 18.310 1.00 0.00 C
|
| 13 |
+
ATOM 10 HA2 GLY A 2 16.700 5.550 18.300 1.00 0.00 H
|
| 14 |
+
ATOM 11 HA3 GLY A 2 17.780 6.940 18.790 1.00 0.00 H
|
| 15 |
+
ATOM 12 C GLY A 2 15.820 6.940 19.360 1.00 0.00 C
|
| 16 |
+
ATOM 13 O GLY A 2 14.670 7.240 18.950 1.00 0.00 O
|
| 17 |
+
ATOM 14 N GLY A 3 16.110 6.750 20.660 1.00 0.00 N
|
| 18 |
+
ATOM 15 H GLY A 3 17.070 6.480 20.850 1.00 0.00 H
|
| 19 |
+
ATOM 16 CA GLY A 3 15.260 6.920 21.860 1.00 0.00 C
|
| 20 |
+
ATOM 17 HA2 GLY A 3 15.380 7.940 22.220 1.00 0.00 H
|
| 21 |
+
ATOM 18 HA3 GLY A 3 14.200 6.740 21.670 1.00 0.00 H
|
| 22 |
+
ATOM 19 C GLY A 3 15.700 6.170 23.090 1.00 0.00 C
|
| 23 |
+
ATOM 20 O GLY A 3 15.410 6.640 24.190 1.00 0.00 O
|
| 24 |
+
ATOM 21 N NME A 4 16.310 5.000 22.940 1.00 0.00 N
|
| 25 |
+
ATOM 22 H NME A 4 16.680 4.680 22.050 1.00 0.00 H
|
| 26 |
+
ATOM 23 C NME A 4 16.470 3.900 23.950 1.00 0.00 C
|
| 27 |
+
ATOM 24 H1 NME A 4 17.210 4.220 24.680 1.00 0.00 H
|
| 28 |
+
ATOM 25 H2 NME A 4 15.550 3.700 24.510 1.00 0.00 H
|
| 29 |
+
ATOM 26 H3 NME A 4 16.790 2.970 23.470 1.00 0.00 H
|
| 30 |
+
TER 27 NME A 4
|
| 31 |
+
ENDMDL
|
| 32 |
+
CONECT 1 2
|
| 33 |
+
CONECT 2 5 1 3 4
|
| 34 |
+
CONECT 3 2
|
| 35 |
+
CONECT 4 2
|
| 36 |
+
CONECT 5 2 6 7
|
| 37 |
+
CONECT 6 5
|
| 38 |
+
CONECT 7 5
|
| 39 |
+
CONECT 19 21
|
| 40 |
+
CONECT 21 19 23 22
|
| 41 |
+
CONECT 22 21
|
| 42 |
+
CONECT 23 24 25 26 21
|
| 43 |
+
CONECT 24 23
|
| 44 |
+
CONECT 25 23
|
| 45 |
+
CONECT 26 23
|
| 46 |
+
END
|
grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/init_structures/gly_gly_grid_0063_0.pdb
ADDED
|
@@ -0,0 +1,46 @@
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
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|
|
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|
|
|
|
|
|
|
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|
|
|
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|
|
|
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|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
REMARK 1 CREATED WITH MDTraj 1.10.3, 2026-03-03
|
| 2 |
+
CRYST1 21.970 21.970 21.970 90.00 90.00 90.00 P 1 1
|
| 3 |
+
MODEL 0
|
| 4 |
+
ATOM 1 H1 ACE A 1 8.760 0.370 13.190 1.00 0.00 H
|
| 5 |
+
ATOM 2 CH3 ACE A 1 8.760 1.310 13.730 1.00 0.00 C
|
| 6 |
+
ATOM 3 H2 ACE A 1 9.360 1.090 14.620 1.00 0.00 H
|
| 7 |
+
ATOM 4 H3 ACE A 1 7.780 1.590 14.130 1.00 0.00 H
|
| 8 |
+
ATOM 5 C ACE A 1 9.420 2.410 12.890 1.00 0.00 C
|
| 9 |
+
ATOM 6 O ACE A 1 10.000 3.410 13.400 1.00 0.00 O
|
| 10 |
+
ATOM 7 N GLY A 2 9.160 2.270 11.560 1.00 0.00 N
|
| 11 |
+
ATOM 8 H GLY A 2 8.560 1.530 11.220 1.00 0.00 H
|
| 12 |
+
ATOM 9 CA GLY A 2 9.830 3.150 10.580 1.00 0.00 C
|
| 13 |
+
ATOM 10 HA2 GLY A 2 9.760 4.170 10.950 1.00 0.00 H
|
| 14 |
+
ATOM 11 HA3 GLY A 2 10.830 2.810 10.320 1.00 0.00 H
|
| 15 |
+
ATOM 12 C GLY A 2 8.990 3.240 9.330 1.00 0.00 C
|
| 16 |
+
ATOM 13 O GLY A 2 7.780 3.110 9.320 1.00 0.00 O
|
| 17 |
+
ATOM 14 N GLY A 3 9.630 3.570 8.200 1.00 0.00 N
|
| 18 |
+
ATOM 15 H GLY A 3 10.580 3.900 8.290 1.00 0.00 H
|
| 19 |
+
ATOM 16 CA GLY A 3 9.110 3.420 6.870 1.00 0.00 C
|
| 20 |
+
ATOM 17 HA2 GLY A 3 9.230 2.370 6.600 1.00 0.00 H
|
| 21 |
+
ATOM 18 HA3 GLY A 3 8.070 3.730 6.790 1.00 0.00 H
|
| 22 |
+
ATOM 19 C GLY A 3 9.980 4.300 5.990 1.00 0.00 C
|
| 23 |
+
ATOM 20 O GLY A 3 10.400 5.360 6.440 1.00 0.00 O
|
| 24 |
+
ATOM 21 N NME A 4 10.010 3.940 4.720 1.00 0.00 N
|
| 25 |
+
ATOM 22 H NME A 4 9.500 3.120 4.420 1.00 0.00 H
|
| 26 |
+
ATOM 23 C NME A 4 10.760 4.630 3.720 1.00 0.00 C
|
| 27 |
+
ATOM 24 H1 NME A 4 11.620 4.070 3.360 1.00 0.00 H
|
| 28 |
+
ATOM 25 H2 NME A 4 10.060 4.960 2.950 1.00 0.00 H
|
| 29 |
+
ATOM 26 H3 NME A 4 11.070 5.590 4.140 1.00 0.00 H
|
| 30 |
+
TER 27 NME A 4
|
| 31 |
+
ENDMDL
|
| 32 |
+
CONECT 1 2
|
| 33 |
+
CONECT 2 5 1 3 4
|
| 34 |
+
CONECT 3 2
|
| 35 |
+
CONECT 4 2
|
| 36 |
+
CONECT 5 2 6 7
|
| 37 |
+
CONECT 6 5
|
| 38 |
+
CONECT 7 5
|
| 39 |
+
CONECT 19 21
|
| 40 |
+
CONECT 21 19 23 22
|
| 41 |
+
CONECT 22 21
|
| 42 |
+
CONECT 23 24 25 26 21
|
| 43 |
+
CONECT 24 23
|
| 44 |
+
CONECT 25 23
|
| 45 |
+
CONECT 26 23
|
| 46 |
+
END
|
grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/init_structures/gly_gly_grid_0080_0.pdb
ADDED
|
@@ -0,0 +1,46 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
REMARK 1 CREATED WITH MDTraj 1.10.3, 2026-03-03
|
| 2 |
+
CRYST1 21.727 21.727 21.727 90.00 90.00 90.00 P 1 1
|
| 3 |
+
MODEL 0
|
| 4 |
+
ATOM 1 H1 ACE A 1 21.400 3.160 18.570 1.00 0.00 H
|
| 5 |
+
ATOM 2 CH3 ACE A 1 21.790 3.020 19.570 1.00 0.00 C
|
| 6 |
+
ATOM 3 H2 ACE A 1 22.530 3.740 19.930 1.00 0.00 H
|
| 7 |
+
ATOM 4 H3 ACE A 1 22.290 2.050 19.490 1.00 0.00 H
|
| 8 |
+
ATOM 5 C ACE A 1 20.510 2.940 20.460 1.00 0.00 C
|
| 9 |
+
ATOM 6 O ACE A 1 20.370 1.940 21.170 1.00 0.00 O
|
| 10 |
+
ATOM 7 N GLY A 2 19.620 3.930 20.450 1.00 0.00 N
|
| 11 |
+
ATOM 8 H GLY A 2 19.860 4.720 19.870 1.00 0.00 H
|
| 12 |
+
ATOM 9 CA GLY A 2 18.500 4.180 21.320 1.00 0.00 C
|
| 13 |
+
ATOM 10 HA2 GLY A 2 17.930 3.270 21.510 1.00 0.00 H
|
| 14 |
+
ATOM 11 HA3 GLY A 2 18.870 4.610 22.250 1.00 0.00 H
|
| 15 |
+
ATOM 12 C GLY A 2 17.540 5.140 20.620 1.00 0.00 C
|
| 16 |
+
ATOM 13 O GLY A 2 17.070 4.820 19.510 1.00 0.00 O
|
| 17 |
+
ATOM 14 N GLY A 3 17.290 6.380 21.080 1.00 0.00 N
|
| 18 |
+
ATOM 15 H GLY A 3 17.850 6.610 21.890 1.00 0.00 H
|
| 19 |
+
ATOM 16 CA GLY A 3 16.700 7.430 20.310 1.00 0.00 C
|
| 20 |
+
ATOM 17 HA2 GLY A 3 15.790 7.010 19.870 1.00 0.00 H
|
| 21 |
+
ATOM 18 HA3 GLY A 3 16.510 8.230 21.020 1.00 0.00 H
|
| 22 |
+
ATOM 19 C GLY A 3 17.610 8.070 19.250 1.00 0.00 C
|
| 23 |
+
ATOM 20 O GLY A 3 18.570 7.440 18.770 1.00 0.00 O
|
| 24 |
+
ATOM 21 N NME A 4 17.380 9.340 18.920 1.00 0.00 N
|
| 25 |
+
ATOM 22 H NME A 4 16.620 9.820 19.370 1.00 0.00 H
|
| 26 |
+
ATOM 23 C NME A 4 18.320 10.190 18.240 1.00 0.00 C
|
| 27 |
+
ATOM 24 H1 NME A 4 17.760 10.870 17.600 1.00 0.00 H
|
| 28 |
+
ATOM 25 H2 NME A 4 18.950 10.670 18.990 1.00 0.00 H
|
| 29 |
+
ATOM 26 H3 NME A 4 18.860 9.530 17.550 1.00 0.00 H
|
| 30 |
+
TER 27 NME A 4
|
| 31 |
+
ENDMDL
|
| 32 |
+
CONECT 1 2
|
| 33 |
+
CONECT 2 5 1 3 4
|
| 34 |
+
CONECT 3 2
|
| 35 |
+
CONECT 4 2
|
| 36 |
+
CONECT 5 2 6 7
|
| 37 |
+
CONECT 6 5
|
| 38 |
+
CONECT 7 5
|
| 39 |
+
CONECT 19 21
|
| 40 |
+
CONECT 21 19 23 22
|
| 41 |
+
CONECT 22 21
|
| 42 |
+
CONECT 23 24 25 26 21
|
| 43 |
+
CONECT 24 23
|
| 44 |
+
CONECT 25 23
|
| 45 |
+
CONECT 26 23
|
| 46 |
+
END
|
grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/init_structures/gly_gly_grid_0083_0.pdb
ADDED
|
@@ -0,0 +1,46 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
REMARK 1 CREATED WITH MDTraj 1.10.3, 2026-03-03
|
| 2 |
+
CRYST1 21.973 21.973 21.973 90.00 90.00 90.00 P 1 1
|
| 3 |
+
MODEL 0
|
| 4 |
+
ATOM 1 H1 ACE A 1 22.840 13.160 11.820 1.00 0.00 H
|
| 5 |
+
ATOM 2 CH3 ACE A 1 23.520 13.200 12.670 1.00 0.00 C
|
| 6 |
+
ATOM 3 H2 ACE A 1 24.290 12.520 12.300 1.00 0.00 H
|
| 7 |
+
ATOM 4 H3 ACE A 1 23.030 12.770 13.550 1.00 0.00 H
|
| 8 |
+
ATOM 5 C ACE A 1 24.180 14.550 13.060 1.00 0.00 C
|
| 9 |
+
ATOM 6 O ACE A 1 25.370 14.720 12.980 1.00 0.00 O
|
| 10 |
+
ATOM 7 N GLY A 2 23.400 15.300 13.800 1.00 0.00 N
|
| 11 |
+
ATOM 8 H GLY A 2 22.500 14.950 14.090 1.00 0.00 H
|
| 12 |
+
ATOM 9 CA GLY A 2 23.680 16.710 14.020 1.00 0.00 C
|
| 13 |
+
ATOM 10 HA2 GLY A 2 24.760 16.870 14.030 1.00 0.00 H
|
| 14 |
+
ATOM 11 HA3 GLY A 2 23.330 17.270 13.160 1.00 0.00 H
|
| 15 |
+
ATOM 12 C GLY A 2 23.100 17.260 15.320 1.00 0.00 C
|
| 16 |
+
ATOM 13 O GLY A 2 23.400 16.760 16.420 1.00 0.00 O
|
| 17 |
+
ATOM 14 N GLY A 3 22.210 18.260 15.220 1.00 0.00 N
|
| 18 |
+
ATOM 15 H GLY A 3 21.850 18.450 14.290 1.00 0.00 H
|
| 19 |
+
ATOM 16 CA GLY A 3 21.370 18.740 16.370 1.00 0.00 C
|
| 20 |
+
ATOM 17 HA2 GLY A 3 21.980 19.010 17.230 1.00 0.00 H
|
| 21 |
+
ATOM 18 HA3 GLY A 3 20.850 19.650 16.090 1.00 0.00 H
|
| 22 |
+
ATOM 19 C GLY A 3 20.210 17.790 16.860 1.00 0.00 C
|
| 23 |
+
ATOM 20 O GLY A 3 19.810 17.880 17.970 1.00 0.00 O
|
| 24 |
+
ATOM 21 N NME A 4 19.720 16.920 15.980 1.00 0.00 N
|
| 25 |
+
ATOM 22 H NME A 4 20.140 16.830 15.060 1.00 0.00 H
|
| 26 |
+
ATOM 23 C NME A 4 18.750 15.900 16.440 1.00 0.00 C
|
| 27 |
+
ATOM 24 H1 NME A 4 19.350 15.030 16.710 1.00 0.00 H
|
| 28 |
+
ATOM 25 H2 NME A 4 18.230 16.190 17.350 1.00 0.00 H
|
| 29 |
+
ATOM 26 H3 NME A 4 18.150 15.590 15.580 1.00 0.00 H
|
| 30 |
+
TER 27 NME A 4
|
| 31 |
+
ENDMDL
|
| 32 |
+
CONECT 1 2
|
| 33 |
+
CONECT 2 5 1 3 4
|
| 34 |
+
CONECT 3 2
|
| 35 |
+
CONECT 4 2
|
| 36 |
+
CONECT 5 2 6 7
|
| 37 |
+
CONECT 6 5
|
| 38 |
+
CONECT 7 5
|
| 39 |
+
CONECT 19 21
|
| 40 |
+
CONECT 21 19 23 22
|
| 41 |
+
CONECT 22 21
|
| 42 |
+
CONECT 23 24 25 26 21
|
| 43 |
+
CONECT 24 23
|
| 44 |
+
CONECT 25 23
|
| 45 |
+
CONECT 26 23
|
| 46 |
+
END
|
grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/init_structures/gly_gly_grid_0087_0.pdb
ADDED
|
@@ -0,0 +1,46 @@
|
|
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|
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|
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|
|
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|
|
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|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
REMARK 1 CREATED WITH MDTraj 1.10.3, 2026-03-03
|
| 2 |
+
CRYST1 21.805 21.805 21.805 90.00 90.00 90.00 P 1 1
|
| 3 |
+
MODEL 0
|
| 4 |
+
ATOM 1 H1 ACE A 1 15.470 8.590 8.850 1.00 0.00 H
|
| 5 |
+
ATOM 2 CH3 ACE A 1 15.990 9.260 8.160 1.00 0.00 C
|
| 6 |
+
ATOM 3 H2 ACE A 1 15.280 9.450 7.360 1.00 0.00 H
|
| 7 |
+
ATOM 4 H3 ACE A 1 16.920 8.820 7.800 1.00 0.00 H
|
| 8 |
+
ATOM 5 C ACE A 1 16.310 10.420 9.040 1.00 0.00 C
|
| 9 |
+
ATOM 6 O ACE A 1 15.640 10.700 10.040 1.00 0.00 O
|
| 10 |
+
ATOM 7 N GLY A 2 17.290 11.210 8.670 1.00 0.00 N
|
| 11 |
+
ATOM 8 H GLY A 2 17.860 10.990 7.870 1.00 0.00 H
|
| 12 |
+
ATOM 9 CA GLY A 2 17.650 12.430 9.350 1.00 0.00 C
|
| 13 |
+
ATOM 10 HA2 GLY A 2 16.870 13.030 9.820 1.00 0.00 H
|
| 14 |
+
ATOM 11 HA3 GLY A 2 18.250 12.130 10.210 1.00 0.00 H
|
| 15 |
+
ATOM 12 C GLY A 2 18.360 13.340 8.320 1.00 0.00 C
|
| 16 |
+
ATOM 13 O GLY A 2 17.790 13.740 7.270 1.00 0.00 O
|
| 17 |
+
ATOM 14 N GLY A 3 19.650 13.710 8.590 1.00 0.00 N
|
| 18 |
+
ATOM 15 H GLY A 3 20.220 13.200 9.240 1.00 0.00 H
|
| 19 |
+
ATOM 16 CA GLY A 3 20.260 14.750 7.870 1.00 0.00 C
|
| 20 |
+
ATOM 17 HA2 GLY A 3 19.570 15.590 7.920 1.00 0.00 H
|
| 21 |
+
ATOM 18 HA3 GLY A 3 21.190 14.890 8.420 1.00 0.00 H
|
| 22 |
+
ATOM 19 C GLY A 3 20.670 14.400 6.370 1.00 0.00 C
|
| 23 |
+
ATOM 20 O GLY A 3 20.780 13.280 5.910 1.00 0.00 O
|
| 24 |
+
ATOM 21 N NME A 4 20.880 15.440 5.540 1.00 0.00 N
|
| 25 |
+
ATOM 22 H NME A 4 20.620 16.350 5.900 1.00 0.00 H
|
| 26 |
+
ATOM 23 C NME A 4 21.530 15.330 4.220 1.00 0.00 C
|
| 27 |
+
ATOM 24 H1 NME A 4 22.240 16.160 4.280 1.00 0.00 H
|
| 28 |
+
ATOM 25 H2 NME A 4 22.150 14.440 4.170 1.00 0.00 H
|
| 29 |
+
ATOM 26 H3 NME A 4 20.840 15.500 3.390 1.00 0.00 H
|
| 30 |
+
TER 27 NME A 4
|
| 31 |
+
ENDMDL
|
| 32 |
+
CONECT 1 2
|
| 33 |
+
CONECT 2 5 1 3 4
|
| 34 |
+
CONECT 3 2
|
| 35 |
+
CONECT 4 2
|
| 36 |
+
CONECT 5 2 6 7
|
| 37 |
+
CONECT 6 5
|
| 38 |
+
CONECT 7 5
|
| 39 |
+
CONECT 19 21
|
| 40 |
+
CONECT 21 19 23 22
|
| 41 |
+
CONECT 22 21
|
| 42 |
+
CONECT 23 24 25 26 21
|
| 43 |
+
CONECT 24 23
|
| 44 |
+
CONECT 25 23
|
| 45 |
+
CONECT 26 23
|
| 46 |
+
END
|
grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/init_structures/gly_gly_grid_0105_0.pdb
ADDED
|
@@ -0,0 +1,46 @@
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
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|
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|
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|
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|
|
|
|
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|
|
|
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|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
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|
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|
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|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
REMARK 1 CREATED WITH MDTraj 1.10.3, 2026-03-03
|
| 2 |
+
CRYST1 21.948 21.948 21.948 90.00 90.00 90.00 P 1 1
|
| 3 |
+
MODEL 0
|
| 4 |
+
ATOM 1 H1 ACE A 1 4.460 25.130 21.210 1.00 0.00 H
|
| 5 |
+
ATOM 2 CH3 ACE A 1 5.430 24.640 21.220 1.00 0.00 C
|
| 6 |
+
ATOM 3 H2 ACE A 1 5.980 24.940 22.110 1.00 0.00 H
|
| 7 |
+
ATOM 4 H3 ACE A 1 5.930 24.880 20.280 1.00 0.00 H
|
| 8 |
+
ATOM 5 C ACE A 1 5.150 23.150 21.220 1.00 0.00 C
|
| 9 |
+
ATOM 6 O ACE A 1 5.910 22.380 21.740 1.00 0.00 O
|
| 10 |
+
ATOM 7 N GLY A 2 3.960 22.760 20.790 1.00 0.00 N
|
| 11 |
+
ATOM 8 H GLY A 2 3.250 23.420 20.490 1.00 0.00 H
|
| 12 |
+
ATOM 9 CA GLY A 2 3.660 21.340 20.550 1.00 0.00 C
|
| 13 |
+
ATOM 10 HA2 GLY A 2 4.520 20.830 20.120 1.00 0.00 H
|
| 14 |
+
ATOM 11 HA3 GLY A 2 3.330 20.880 21.480 1.00 0.00 H
|
| 15 |
+
ATOM 12 C GLY A 2 2.600 21.150 19.410 1.00 0.00 C
|
| 16 |
+
ATOM 13 O GLY A 2 2.900 21.310 18.260 1.00 0.00 O
|
| 17 |
+
ATOM 14 N GLY A 3 1.370 20.830 19.820 1.00 0.00 N
|
| 18 |
+
ATOM 15 H GLY A 3 1.230 20.520 20.770 1.00 0.00 H
|
| 19 |
+
ATOM 16 CA GLY A 3 0.200 20.780 18.850 1.00 0.00 C
|
| 20 |
+
ATOM 17 HA2 GLY A 3 -0.760 20.510 19.280 1.00 0.00 H
|
| 21 |
+
ATOM 18 HA3 GLY A 3 0.200 21.710 18.290 1.00 0.00 H
|
| 22 |
+
ATOM 19 C GLY A 3 0.320 19.710 17.790 1.00 0.00 C
|
| 23 |
+
ATOM 20 O GLY A 3 0.310 18.550 18.190 1.00 0.00 O
|
| 24 |
+
ATOM 21 N NME A 4 0.440 20.020 16.470 1.00 0.00 N
|
| 25 |
+
ATOM 22 H NME A 4 0.390 20.970 16.140 1.00 0.00 H
|
| 26 |
+
ATOM 23 C NME A 4 0.350 18.910 15.560 1.00 0.00 C
|
| 27 |
+
ATOM 24 H1 NME A 4 1.290 18.360 15.670 1.00 0.00 H
|
| 28 |
+
ATOM 25 H2 NME A 4 -0.310 18.080 15.830 1.00 0.00 H
|
| 29 |
+
ATOM 26 H3 NME A 4 0.240 19.190 14.520 1.00 0.00 H
|
| 30 |
+
TER 27 NME A 4
|
| 31 |
+
ENDMDL
|
| 32 |
+
CONECT 1 2
|
| 33 |
+
CONECT 2 5 1 3 4
|
| 34 |
+
CONECT 3 2
|
| 35 |
+
CONECT 4 2
|
| 36 |
+
CONECT 5 2 6 7
|
| 37 |
+
CONECT 6 5
|
| 38 |
+
CONECT 7 5
|
| 39 |
+
CONECT 19 21
|
| 40 |
+
CONECT 21 19 23 22
|
| 41 |
+
CONECT 22 21
|
| 42 |
+
CONECT 23 24 25 26 21
|
| 43 |
+
CONECT 24 23
|
| 44 |
+
CONECT 25 23
|
| 45 |
+
CONECT 26 23
|
| 46 |
+
END
|
grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/init_structures/gly_gly_grid_0108_0.pdb
ADDED
|
@@ -0,0 +1,46 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
REMARK 1 CREATED WITH MDTraj 1.10.3, 2026-03-03
|
| 2 |
+
CRYST1 21.770 21.770 21.770 90.00 90.00 90.00 P 1 1
|
| 3 |
+
MODEL 0
|
| 4 |
+
ATOM 1 H1 ACE A 1 7.200 3.190 18.540 1.00 0.00 H
|
| 5 |
+
ATOM 2 CH3 ACE A 1 6.350 3.870 18.540 1.00 0.00 C
|
| 6 |
+
ATOM 3 H2 ACE A 1 6.220 4.070 19.610 1.00 0.00 H
|
| 7 |
+
ATOM 4 H3 ACE A 1 5.460 3.360 18.180 1.00 0.00 H
|
| 8 |
+
ATOM 5 C ACE A 1 6.550 5.080 17.600 1.00 0.00 C
|
| 9 |
+
ATOM 6 O ACE A 1 5.830 5.100 16.610 1.00 0.00 O
|
| 10 |
+
ATOM 7 N GLY A 2 7.530 5.960 17.870 1.00 0.00 N
|
| 11 |
+
ATOM 8 H GLY A 2 8.060 5.780 18.710 1.00 0.00 H
|
| 12 |
+
ATOM 9 CA GLY A 2 8.110 6.920 16.860 1.00 0.00 C
|
| 13 |
+
ATOM 10 HA2 GLY A 2 8.250 6.340 15.950 1.00 0.00 H
|
| 14 |
+
ATOM 11 HA3 GLY A 2 7.530 7.830 16.760 1.00 0.00 H
|
| 15 |
+
ATOM 12 C GLY A 2 9.470 7.240 17.420 1.00 0.00 C
|
| 16 |
+
ATOM 13 O GLY A 2 10.280 6.350 17.440 1.00 0.00 O
|
| 17 |
+
ATOM 14 N GLY A 3 9.720 8.450 17.930 1.00 0.00 N
|
| 18 |
+
ATOM 15 H GLY A 3 8.940 9.090 18.030 1.00 0.00 H
|
| 19 |
+
ATOM 16 CA GLY A 3 10.980 8.690 18.550 1.00 0.00 C
|
| 20 |
+
ATOM 17 HA2 GLY A 3 10.990 9.650 19.070 1.00 0.00 H
|
| 21 |
+
ATOM 18 HA3 GLY A 3 11.110 7.940 19.340 1.00 0.00 H
|
| 22 |
+
ATOM 19 C GLY A 3 12.300 8.670 17.720 1.00 0.00 C
|
| 23 |
+
ATOM 20 O GLY A 3 13.370 8.310 18.210 1.00 0.00 O
|
| 24 |
+
ATOM 21 N NME A 4 12.300 9.020 16.410 1.00 0.00 N
|
| 25 |
+
ATOM 22 H NME A 4 11.470 9.450 16.050 1.00 0.00 H
|
| 26 |
+
ATOM 23 C NME A 4 13.510 9.070 15.540 1.00 0.00 C
|
| 27 |
+
ATOM 24 H1 NME A 4 14.240 8.400 16.000 1.00 0.00 H
|
| 28 |
+
ATOM 25 H2 NME A 4 13.260 8.730 14.540 1.00 0.00 H
|
| 29 |
+
ATOM 26 H3 NME A 4 13.920 10.080 15.480 1.00 0.00 H
|
| 30 |
+
TER 27 NME A 4
|
| 31 |
+
ENDMDL
|
| 32 |
+
CONECT 1 2
|
| 33 |
+
CONECT 2 5 1 3 4
|
| 34 |
+
CONECT 3 2
|
| 35 |
+
CONECT 4 2
|
| 36 |
+
CONECT 5 2 6 7
|
| 37 |
+
CONECT 6 5
|
| 38 |
+
CONECT 7 5
|
| 39 |
+
CONECT 19 21
|
| 40 |
+
CONECT 21 19 23 22
|
| 41 |
+
CONECT 22 21
|
| 42 |
+
CONECT 23 24 25 26 21
|
| 43 |
+
CONECT 24 23
|
| 44 |
+
CONECT 25 23
|
| 45 |
+
CONECT 26 23
|
| 46 |
+
END
|
grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/init_structures/gly_gly_grid_0111_0.pdb
ADDED
|
@@ -0,0 +1,46 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
REMARK 1 CREATED WITH MDTraj 1.10.3, 2026-03-03
|
| 2 |
+
CRYST1 21.926 21.926 21.926 90.00 90.00 90.00 P 1 1
|
| 3 |
+
MODEL 0
|
| 4 |
+
ATOM 1 H1 ACE A 1 10.810 0.840 13.260 1.00 0.00 H
|
| 5 |
+
ATOM 2 CH3 ACE A 1 11.440 1.730 13.190 1.00 0.00 C
|
| 6 |
+
ATOM 3 H2 ACE A 1 11.590 2.160 14.180 1.00 0.00 H
|
| 7 |
+
ATOM 4 H3 ACE A 1 11.150 2.470 12.450 1.00 0.00 H
|
| 8 |
+
ATOM 5 C ACE A 1 12.810 1.270 12.630 1.00 0.00 C
|
| 9 |
+
ATOM 6 O ACE A 1 13.840 1.470 13.210 1.00 0.00 O
|
| 10 |
+
ATOM 7 N GLY A 2 12.790 0.860 11.380 1.00 0.00 N
|
| 11 |
+
ATOM 8 H GLY A 2 11.890 0.760 10.930 1.00 0.00 H
|
| 12 |
+
ATOM 9 CA GLY A 2 13.910 0.370 10.590 1.00 0.00 C
|
| 13 |
+
ATOM 10 HA2 GLY A 2 14.870 0.780 10.920 1.00 0.00 H
|
| 14 |
+
ATOM 11 HA3 GLY A 2 14.000 -0.650 10.980 1.00 0.00 H
|
| 15 |
+
ATOM 12 C GLY A 2 13.790 0.520 9.060 1.00 0.00 C
|
| 16 |
+
ATOM 13 O GLY A 2 14.000 1.610 8.560 1.00 0.00 O
|
| 17 |
+
ATOM 14 N GLY A 3 13.690 -0.620 8.330 1.00 0.00 N
|
| 18 |
+
ATOM 15 H GLY A 3 13.780 -1.490 8.840 1.00 0.00 H
|
| 19 |
+
ATOM 16 CA GLY A 3 13.850 -0.660 6.880 1.00 0.00 C
|
| 20 |
+
ATOM 17 HA2 GLY A 3 13.500 -1.610 6.460 1.00 0.00 H
|
| 21 |
+
ATOM 18 HA3 GLY A 3 13.200 0.110 6.440 1.00 0.00 H
|
| 22 |
+
ATOM 19 C GLY A 3 15.260 -0.440 6.370 1.00 0.00 C
|
| 23 |
+
ATOM 20 O GLY A 3 16.140 -0.050 7.090 1.00 0.00 O
|
| 24 |
+
ATOM 21 N NME A 4 15.400 -0.670 5.050 1.00 0.00 N
|
| 25 |
+
ATOM 22 H NME A 4 14.670 -1.090 4.500 1.00 0.00 H
|
| 26 |
+
ATOM 23 C NME A 4 16.700 -0.490 4.330 1.00 0.00 C
|
| 27 |
+
ATOM 24 H1 NME A 4 16.470 -0.120 3.330 1.00 0.00 H
|
| 28 |
+
ATOM 25 H2 NME A 4 17.330 0.250 4.830 1.00 0.00 H
|
| 29 |
+
ATOM 26 H3 NME A 4 17.190 -1.460 4.430 1.00 0.00 H
|
| 30 |
+
TER 27 NME A 4
|
| 31 |
+
ENDMDL
|
| 32 |
+
CONECT 1 2
|
| 33 |
+
CONECT 2 5 1 3 4
|
| 34 |
+
CONECT 3 2
|
| 35 |
+
CONECT 4 2
|
| 36 |
+
CONECT 5 2 6 7
|
| 37 |
+
CONECT 6 5
|
| 38 |
+
CONECT 7 5
|
| 39 |
+
CONECT 19 21
|
| 40 |
+
CONECT 21 19 23 22
|
| 41 |
+
CONECT 22 21
|
| 42 |
+
CONECT 23 24 25 26 21
|
| 43 |
+
CONECT 24 23
|
| 44 |
+
CONECT 25 23
|
| 45 |
+
CONECT 26 23
|
| 46 |
+
END
|
grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/init_structures/gly_gly_grid_0120_0.pdb
ADDED
|
@@ -0,0 +1,46 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
REMARK 1 CREATED WITH MDTraj 1.10.3, 2026-03-03
|
| 2 |
+
CRYST1 21.963 21.963 21.963 90.00 90.00 90.00 P 1 1
|
| 3 |
+
MODEL 0
|
| 4 |
+
ATOM 1 H1 ACE A 1 19.420 8.380 7.410 1.00 0.00 H
|
| 5 |
+
ATOM 2 CH3 ACE A 1 19.770 7.810 6.550 1.00 0.00 C
|
| 6 |
+
ATOM 3 H2 ACE A 1 20.860 7.720 6.520 1.00 0.00 H
|
| 7 |
+
ATOM 4 H3 ACE A 1 19.430 8.260 5.610 1.00 0.00 H
|
| 8 |
+
ATOM 5 C ACE A 1 19.200 6.390 6.660 1.00 0.00 C
|
| 9 |
+
ATOM 6 O ACE A 1 19.870 5.450 6.190 1.00 0.00 O
|
| 10 |
+
ATOM 7 N GLY A 2 18.020 6.270 7.120 1.00 0.00 N
|
| 11 |
+
ATOM 8 H GLY A 2 17.500 6.950 7.640 1.00 0.00 H
|
| 12 |
+
ATOM 9 CA GLY A 2 17.270 5.050 6.890 1.00 0.00 C
|
| 13 |
+
ATOM 10 HA2 GLY A 2 17.430 4.750 5.850 1.00 0.00 H
|
| 14 |
+
ATOM 11 HA3 GLY A 2 17.530 4.180 7.500 1.00 0.00 H
|
| 15 |
+
ATOM 12 C GLY A 2 15.820 5.410 7.050 1.00 0.00 C
|
| 16 |
+
ATOM 13 O GLY A 2 15.290 6.120 6.180 1.00 0.00 O
|
| 17 |
+
ATOM 14 N GLY A 3 15.140 4.830 8.040 1.00 0.00 N
|
| 18 |
+
ATOM 15 H GLY A 3 15.640 4.250 8.710 1.00 0.00 H
|
| 19 |
+
ATOM 16 CA GLY A 3 13.740 5.040 8.290 1.00 0.00 C
|
| 20 |
+
ATOM 17 HA2 GLY A 3 13.570 5.920 8.910 1.00 0.00 H
|
| 21 |
+
ATOM 18 HA3 GLY A 3 13.300 5.110 7.300 1.00 0.00 H
|
| 22 |
+
ATOM 19 C GLY A 3 13.120 3.880 9.080 1.00 0.00 C
|
| 23 |
+
ATOM 20 O GLY A 3 13.830 3.100 9.660 1.00 0.00 O
|
| 24 |
+
ATOM 21 N NME A 4 11.770 3.790 8.930 1.00 0.00 N
|
| 25 |
+
ATOM 22 H NME A 4 11.340 4.410 8.260 1.00 0.00 H
|
| 26 |
+
ATOM 23 C NME A 4 10.860 2.870 9.710 1.00 0.00 C
|
| 27 |
+
ATOM 24 H1 NME A 4 9.930 2.770 9.150 1.00 0.00 H
|
| 28 |
+
ATOM 25 H2 NME A 4 11.320 1.900 9.900 1.00 0.00 H
|
| 29 |
+
ATOM 26 H3 NME A 4 10.530 3.280 10.660 1.00 0.00 H
|
| 30 |
+
TER 27 NME A 4
|
| 31 |
+
ENDMDL
|
| 32 |
+
CONECT 1 2
|
| 33 |
+
CONECT 2 5 1 3 4
|
| 34 |
+
CONECT 3 2
|
| 35 |
+
CONECT 4 2
|
| 36 |
+
CONECT 5 2 6 7
|
| 37 |
+
CONECT 6 5
|
| 38 |
+
CONECT 7 5
|
| 39 |
+
CONECT 19 21
|
| 40 |
+
CONECT 21 19 23 22
|
| 41 |
+
CONECT 22 21
|
| 42 |
+
CONECT 23 24 25 26 21
|
| 43 |
+
CONECT 24 23
|
| 44 |
+
CONECT 25 23
|
| 45 |
+
CONECT 26 23
|
| 46 |
+
END
|
grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/init_structures/gly_gly_grid_0147_0.pdb
ADDED
|
@@ -0,0 +1,46 @@
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
REMARK 1 CREATED WITH MDTraj 1.10.3, 2026-03-03
|
| 2 |
+
CRYST1 21.906 21.906 21.906 90.00 90.00 90.00 P 1 1
|
| 3 |
+
MODEL 0
|
| 4 |
+
ATOM 1 H1 ACE A 1 24.240 10.830 13.510 1.00 0.00 H
|
| 5 |
+
ATOM 2 CH3 ACE A 1 23.290 11.120 13.960 1.00 0.00 C
|
| 6 |
+
ATOM 3 H2 ACE A 1 23.420 11.840 14.770 1.00 0.00 H
|
| 7 |
+
ATOM 4 H3 ACE A 1 22.820 10.200 14.300 1.00 0.00 H
|
| 8 |
+
ATOM 5 C ACE A 1 22.580 11.860 12.920 1.00 0.00 C
|
| 9 |
+
ATOM 6 O ACE A 1 22.910 13.070 12.820 1.00 0.00 O
|
| 10 |
+
ATOM 7 N GLY A 2 21.640 11.190 12.290 1.00 0.00 N
|
| 11 |
+
ATOM 8 H GLY A 2 21.500 10.250 12.650 1.00 0.00 H
|
| 12 |
+
ATOM 9 CA GLY A 2 20.640 11.720 11.270 1.00 0.00 C
|
| 13 |
+
ATOM 10 HA2 GLY A 2 20.370 12.740 11.570 1.00 0.00 H
|
| 14 |
+
ATOM 11 HA3 GLY A 2 21.140 11.730 10.310 1.00 0.00 H
|
| 15 |
+
ATOM 12 C GLY A 2 19.290 10.960 11.100 1.00 0.00 C
|
| 16 |
+
ATOM 13 O GLY A 2 18.250 11.500 11.420 1.00 0.00 O
|
| 17 |
+
ATOM 14 N GLY A 3 19.420 9.720 10.700 1.00 0.00 N
|
| 18 |
+
ATOM 15 H GLY A 3 20.340 9.300 10.690 1.00 0.00 H
|
| 19 |
+
ATOM 16 CA GLY A 3 18.370 8.760 10.330 1.00 0.00 C
|
| 20 |
+
ATOM 17 HA2 GLY A 3 17.750 9.190 9.540 1.00 0.00 H
|
| 21 |
+
ATOM 18 HA3 GLY A 3 18.770 7.880 9.840 1.00 0.00 H
|
| 22 |
+
ATOM 19 C GLY A 3 17.460 8.290 11.500 1.00 0.00 C
|
| 23 |
+
ATOM 20 O GLY A 3 16.420 7.730 11.170 1.00 0.00 O
|
| 24 |
+
ATOM 21 N NME A 4 17.880 8.370 12.810 1.00 0.00 N
|
| 25 |
+
ATOM 22 H NME A 4 18.780 8.800 12.970 1.00 0.00 H
|
| 26 |
+
ATOM 23 C NME A 4 16.890 8.020 13.910 1.00 0.00 C
|
| 27 |
+
ATOM 24 H1 NME A 4 16.220 8.820 14.200 1.00 0.00 H
|
| 28 |
+
ATOM 25 H2 NME A 4 16.270 7.160 13.650 1.00 0.00 H
|
| 29 |
+
ATOM 26 H3 NME A 4 17.440 7.790 14.830 1.00 0.00 H
|
| 30 |
+
TER 27 NME A 4
|
| 31 |
+
ENDMDL
|
| 32 |
+
CONECT 1 2
|
| 33 |
+
CONECT 2 5 1 3 4
|
| 34 |
+
CONECT 3 2
|
| 35 |
+
CONECT 4 2
|
| 36 |
+
CONECT 5 2 6 7
|
| 37 |
+
CONECT 6 5
|
| 38 |
+
CONECT 7 5
|
| 39 |
+
CONECT 19 21
|
| 40 |
+
CONECT 21 19 23 22
|
| 41 |
+
CONECT 22 21
|
| 42 |
+
CONECT 23 24 25 26 21
|
| 43 |
+
CONECT 24 23
|
| 44 |
+
CONECT 25 23
|
| 45 |
+
CONECT 26 23
|
| 46 |
+
END
|
grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/init_structures/gly_gly_grid_0148_0.pdb
ADDED
|
@@ -0,0 +1,46 @@
|
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|
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|
|
|
|
|
|
|
|
|
|
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|
|
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|
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|
|
|
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|
|
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|
|
|
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|
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|
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|
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|
|
|
|
|
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|
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|
|
|
|
|
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|
|
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|
|
|
|
|
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|
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|
|
|
|
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|
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|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
REMARK 1 CREATED WITH MDTraj 1.10.3, 2026-03-03
|
| 2 |
+
CRYST1 21.839 21.839 21.839 90.00 90.00 90.00 P 1 1
|
| 3 |
+
MODEL 0
|
| 4 |
+
ATOM 1 H1 ACE A 1 23.410 9.480 14.000 1.00 0.00 H
|
| 5 |
+
ATOM 2 CH3 ACE A 1 23.930 10.440 13.930 1.00 0.00 C
|
| 6 |
+
ATOM 3 H2 ACE A 1 24.650 10.320 13.120 1.00 0.00 H
|
| 7 |
+
ATOM 4 H3 ACE A 1 24.310 10.830 14.870 1.00 0.00 H
|
| 8 |
+
ATOM 5 C ACE A 1 22.990 11.350 13.230 1.00 0.00 C
|
| 9 |
+
ATOM 6 O ACE A 1 23.170 12.560 13.270 1.00 0.00 O
|
| 10 |
+
ATOM 7 N GLY A 2 21.970 10.790 12.550 1.00 0.00 N
|
| 11 |
+
ATOM 8 H GLY A 2 21.810 9.810 12.700 1.00 0.00 H
|
| 12 |
+
ATOM 9 CA GLY A 2 21.040 11.540 11.710 1.00 0.00 C
|
| 13 |
+
ATOM 10 HA2 GLY A 2 20.820 12.540 12.100 1.00 0.00 H
|
| 14 |
+
ATOM 11 HA3 GLY A 2 21.560 11.730 10.770 1.00 0.00 H
|
| 15 |
+
ATOM 12 C GLY A 2 19.720 10.850 11.340 1.00 0.00 C
|
| 16 |
+
ATOM 13 O GLY A 2 18.630 11.410 11.560 1.00 0.00 O
|
| 17 |
+
ATOM 14 N GLY A 3 19.800 9.700 10.640 1.00 0.00 N
|
| 18 |
+
ATOM 15 H GLY A 3 20.700 9.310 10.420 1.00 0.00 H
|
| 19 |
+
ATOM 16 CA GLY A 3 18.640 8.910 10.260 1.00 0.00 C
|
| 20 |
+
ATOM 17 HA2 GLY A 3 17.890 9.540 9.780 1.00 0.00 H
|
| 21 |
+
ATOM 18 HA3 GLY A 3 18.950 8.310 9.400 1.00 0.00 H
|
| 22 |
+
ATOM 19 C GLY A 3 17.990 8.090 11.380 1.00 0.00 C
|
| 23 |
+
ATOM 20 O GLY A 3 17.450 7.020 11.100 1.00 0.00 O
|
| 24 |
+
ATOM 21 N NME A 4 18.120 8.460 12.700 1.00 0.00 N
|
| 25 |
+
ATOM 22 H NME A 4 18.690 9.270 12.880 1.00 0.00 H
|
| 26 |
+
ATOM 23 C NME A 4 17.650 7.760 13.920 1.00 0.00 C
|
| 27 |
+
ATOM 24 H1 NME A 4 16.600 7.470 13.970 1.00 0.00 H
|
| 28 |
+
ATOM 25 H2 NME A 4 18.230 6.840 14.040 1.00 0.00 H
|
| 29 |
+
ATOM 26 H3 NME A 4 17.830 8.440 14.750 1.00 0.00 H
|
| 30 |
+
TER 27 NME A 4
|
| 31 |
+
ENDMDL
|
| 32 |
+
CONECT 1 2
|
| 33 |
+
CONECT 2 5 1 3 4
|
| 34 |
+
CONECT 3 2
|
| 35 |
+
CONECT 4 2
|
| 36 |
+
CONECT 5 2 6 7
|
| 37 |
+
CONECT 6 5
|
| 38 |
+
CONECT 7 5
|
| 39 |
+
CONECT 19 21
|
| 40 |
+
CONECT 21 19 23 22
|
| 41 |
+
CONECT 22 21
|
| 42 |
+
CONECT 23 24 25 26 21
|
| 43 |
+
CONECT 24 23
|
| 44 |
+
CONECT 25 23
|
| 45 |
+
CONECT 26 23
|
| 46 |
+
END
|
grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/init_structures/gly_gly_grid_0150_0.pdb
ADDED
|
@@ -0,0 +1,46 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
REMARK 1 CREATED WITH MDTraj 1.10.3, 2026-03-03
|
| 2 |
+
CRYST1 21.786 21.786 21.786 90.00 90.00 90.00 P 1 1
|
| 3 |
+
MODEL 0
|
| 4 |
+
ATOM 1 H1 ACE A 1 3.340 24.460 13.110 1.00 0.00 H
|
| 5 |
+
ATOM 2 CH3 ACE A 1 3.310 24.390 12.030 1.00 0.00 C
|
| 6 |
+
ATOM 3 H2 ACE A 1 3.980 25.060 11.490 1.00 0.00 H
|
| 7 |
+
ATOM 4 H3 ACE A 1 2.270 24.710 11.880 1.00 0.00 H
|
| 8 |
+
ATOM 5 C ACE A 1 3.610 23.000 11.570 1.00 0.00 C
|
| 9 |
+
ATOM 6 O ACE A 1 4.410 22.830 10.660 1.00 0.00 O
|
| 10 |
+
ATOM 7 N GLY A 2 2.930 22.090 12.250 1.00 0.00 N
|
| 11 |
+
ATOM 8 H GLY A 2 2.180 22.360 12.860 1.00 0.00 H
|
| 12 |
+
ATOM 9 CA GLY A 2 3.060 20.610 11.890 1.00 0.00 C
|
| 13 |
+
ATOM 10 HA2 GLY A 2 3.020 20.580 10.800 1.00 0.00 H
|
| 14 |
+
ATOM 11 HA3 GLY A 2 4.000 20.090 12.080 1.00 0.00 H
|
| 15 |
+
ATOM 12 C GLY A 2 1.920 19.850 12.490 1.00 0.00 C
|
| 16 |
+
ATOM 13 O GLY A 2 0.980 19.530 11.760 1.00 0.00 O
|
| 17 |
+
ATOM 14 N GLY A 3 1.910 19.690 13.790 1.00 0.00 N
|
| 18 |
+
ATOM 15 H GLY A 3 2.720 20.070 14.260 1.00 0.00 H
|
| 19 |
+
ATOM 16 CA GLY A 3 0.910 19.050 14.680 1.00 0.00 C
|
| 20 |
+
ATOM 17 HA2 GLY A 3 0.770 17.970 14.570 1.00 0.00 H
|
| 21 |
+
ATOM 18 HA3 GLY A 3 1.230 19.320 15.690 1.00 0.00 H
|
| 22 |
+
ATOM 19 C GLY A 3 -0.470 19.770 14.610 1.00 0.00 C
|
| 23 |
+
ATOM 20 O GLY A 3 -0.580 20.890 15.100 1.00 0.00 O
|
| 24 |
+
ATOM 21 N NME A 4 -1.420 19.160 13.980 1.00 0.00 N
|
| 25 |
+
ATOM 22 H NME A 4 -1.280 18.190 13.750 1.00 0.00 H
|
| 26 |
+
ATOM 23 C NME A 4 -2.680 19.780 13.650 1.00 0.00 C
|
| 27 |
+
ATOM 24 H1 NME A 4 -3.120 20.230 14.530 1.00 0.00 H
|
| 28 |
+
ATOM 25 H2 NME A 4 -2.510 20.560 12.910 1.00 0.00 H
|
| 29 |
+
ATOM 26 H3 NME A 4 -3.290 18.990 13.210 1.00 0.00 H
|
| 30 |
+
TER 27 NME A 4
|
| 31 |
+
ENDMDL
|
| 32 |
+
CONECT 1 2
|
| 33 |
+
CONECT 2 5 1 3 4
|
| 34 |
+
CONECT 3 2
|
| 35 |
+
CONECT 4 2
|
| 36 |
+
CONECT 5 2 6 7
|
| 37 |
+
CONECT 6 5
|
| 38 |
+
CONECT 7 5
|
| 39 |
+
CONECT 19 21
|
| 40 |
+
CONECT 21 19 23 22
|
| 41 |
+
CONECT 22 21
|
| 42 |
+
CONECT 23 24 25 26 21
|
| 43 |
+
CONECT 24 23
|
| 44 |
+
CONECT 25 23
|
| 45 |
+
CONECT 26 23
|
| 46 |
+
END
|
grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/init_structures/gly_gly_grid_0196_0.pdb
ADDED
|
@@ -0,0 +1,46 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
REMARK 1 CREATED WITH MDTraj 1.10.3, 2026-03-03
|
| 2 |
+
CRYST1 22.107 22.107 22.107 90.00 90.00 90.00 P 1 1
|
| 3 |
+
MODEL 0
|
| 4 |
+
ATOM 1 H1 ACE A 1 24.100 20.980 21.270 1.00 0.00 H
|
| 5 |
+
ATOM 2 CH3 ACE A 1 23.260 20.320 21.510 1.00 0.00 C
|
| 6 |
+
ATOM 3 H2 ACE A 1 22.460 21.010 21.780 1.00 0.00 H
|
| 7 |
+
ATOM 4 H3 ACE A 1 23.600 19.720 22.350 1.00 0.00 H
|
| 8 |
+
ATOM 5 C ACE A 1 22.860 19.380 20.430 1.00 0.00 C
|
| 9 |
+
ATOM 6 O ACE A 1 23.500 19.300 19.370 1.00 0.00 O
|
| 10 |
+
ATOM 7 N GLY A 2 21.730 18.660 20.680 1.00 0.00 N
|
| 11 |
+
ATOM 8 H GLY A 2 21.330 18.810 21.590 1.00 0.00 H
|
| 12 |
+
ATOM 9 CA GLY A 2 21.110 17.880 19.620 1.00 0.00 C
|
| 13 |
+
ATOM 10 HA2 GLY A 2 21.260 18.340 18.650 1.00 0.00 H
|
| 14 |
+
ATOM 11 HA3 GLY A 2 21.690 16.950 19.650 1.00 0.00 H
|
| 15 |
+
ATOM 12 C GLY A 2 19.650 17.480 19.790 1.00 0.00 C
|
| 16 |
+
ATOM 13 O GLY A 2 19.030 17.240 18.770 1.00 0.00 O
|
| 17 |
+
ATOM 14 N GLY A 3 19.070 17.560 21.000 1.00 0.00 N
|
| 18 |
+
ATOM 15 H GLY A 3 19.620 17.870 21.780 1.00 0.00 H
|
| 19 |
+
ATOM 16 CA GLY A 3 17.690 17.000 21.230 1.00 0.00 C
|
| 20 |
+
ATOM 17 HA2 GLY A 3 17.030 17.400 20.470 1.00 0.00 H
|
| 21 |
+
ATOM 18 HA3 GLY A 3 17.690 15.910 21.150 1.00 0.00 H
|
| 22 |
+
ATOM 19 C GLY A 3 17.000 17.440 22.520 1.00 0.00 C
|
| 23 |
+
ATOM 20 O GLY A 3 16.070 16.750 22.910 1.00 0.00 O
|
| 24 |
+
ATOM 21 N NME A 4 17.340 18.580 23.200 1.00 0.00 N
|
| 25 |
+
ATOM 22 H NME A 4 18.170 19.000 22.810 1.00 0.00 H
|
| 26 |
+
ATOM 23 C NME A 4 16.730 19.040 24.400 1.00 0.00 C
|
| 27 |
+
ATOM 24 H1 NME A 4 17.450 18.870 25.210 1.00 0.00 H
|
| 28 |
+
ATOM 25 H2 NME A 4 16.430 20.090 24.360 1.00 0.00 H
|
| 29 |
+
ATOM 26 H3 NME A 4 15.910 18.390 24.720 1.00 0.00 H
|
| 30 |
+
TER 27 NME A 4
|
| 31 |
+
ENDMDL
|
| 32 |
+
CONECT 1 2
|
| 33 |
+
CONECT 2 5 1 3 4
|
| 34 |
+
CONECT 3 2
|
| 35 |
+
CONECT 4 2
|
| 36 |
+
CONECT 5 2 6 7
|
| 37 |
+
CONECT 6 5
|
| 38 |
+
CONECT 7 5
|
| 39 |
+
CONECT 19 21
|
| 40 |
+
CONECT 21 19 23 22
|
| 41 |
+
CONECT 22 21
|
| 42 |
+
CONECT 23 24 25 26 21
|
| 43 |
+
CONECT 24 23
|
| 44 |
+
CONECT 25 23
|
| 45 |
+
CONECT 26 23
|
| 46 |
+
END
|
grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/init_structures/gly_gly_grid_0200_0.pdb
ADDED
|
@@ -0,0 +1,46 @@
|
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|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
| 1 |
+
REMARK 1 CREATED WITH MDTraj 1.10.3, 2026-03-03
|
| 2 |
+
CRYST1 21.902 21.902 21.902 90.00 90.00 90.00 P 1 1
|
| 3 |
+
MODEL 0
|
| 4 |
+
ATOM 1 H1 ACE A 1 10.550 7.720 26.570 1.00 0.00 H
|
| 5 |
+
ATOM 2 CH3 ACE A 1 10.670 7.180 25.630 1.00 0.00 C
|
| 6 |
+
ATOM 3 H2 ACE A 1 9.790 6.570 25.420 1.00 0.00 H
|
| 7 |
+
ATOM 4 H3 ACE A 1 11.440 6.410 25.710 1.00 0.00 H
|
| 8 |
+
ATOM 5 C ACE A 1 10.920 8.230 24.640 1.00 0.00 C
|
| 9 |
+
ATOM 6 O ACE A 1 10.990 9.470 24.940 1.00 0.00 O
|
| 10 |
+
ATOM 7 N GLY A 2 11.180 7.820 23.370 1.00 0.00 N
|
| 11 |
+
ATOM 8 H GLY A 2 11.190 6.820 23.180 1.00 0.00 H
|
| 12 |
+
ATOM 9 CA GLY A 2 11.600 8.720 22.320 1.00 0.00 C
|
| 13 |
+
ATOM 10 HA2 GLY A 2 11.030 9.650 22.370 1.00 0.00 H
|
| 14 |
+
ATOM 11 HA3 GLY A 2 12.620 9.050 22.540 1.00 0.00 H
|
| 15 |
+
ATOM 12 C GLY A 2 11.520 8.270 20.880 1.00 0.00 C
|
| 16 |
+
ATOM 13 O GLY A 2 11.670 9.100 19.960 1.00 0.00 O
|
| 17 |
+
ATOM 14 N GLY A 3 11.390 6.950 20.740 1.00 0.00 N
|
| 18 |
+
ATOM 15 H GLY A 3 11.200 6.410 21.580 1.00 0.00 H
|
| 19 |
+
ATOM 16 CA GLY A 3 11.340 6.210 19.510 1.00 0.00 C
|
| 20 |
+
ATOM 17 HA2 GLY A 3 11.690 6.770 18.640 1.00 0.00 H
|
| 21 |
+
ATOM 18 HA3 GLY A 3 12.000 5.340 19.560 1.00 0.00 H
|
| 22 |
+
ATOM 19 C GLY A 3 9.910 5.670 19.290 1.00 0.00 C
|
| 23 |
+
ATOM 20 O GLY A 3 8.920 6.140 19.860 1.00 0.00 O
|
| 24 |
+
ATOM 21 N NME A 4 9.910 4.660 18.420 1.00 0.00 N
|
| 25 |
+
ATOM 22 H NME A 4 10.820 4.370 18.090 1.00 0.00 H
|
| 26 |
+
ATOM 23 C NME A 4 8.750 3.900 17.970 1.00 0.00 C
|
| 27 |
+
ATOM 24 H1 NME A 4 8.410 3.210 18.740 1.00 0.00 H
|
| 28 |
+
ATOM 25 H2 NME A 4 7.970 4.590 17.640 1.00 0.00 H
|
| 29 |
+
ATOM 26 H3 NME A 4 9.180 3.260 17.190 1.00 0.00 H
|
| 30 |
+
TER 27 NME A 4
|
| 31 |
+
ENDMDL
|
| 32 |
+
CONECT 1 2
|
| 33 |
+
CONECT 2 5 1 3 4
|
| 34 |
+
CONECT 3 2
|
| 35 |
+
CONECT 4 2
|
| 36 |
+
CONECT 5 2 6 7
|
| 37 |
+
CONECT 6 5
|
| 38 |
+
CONECT 7 5
|
| 39 |
+
CONECT 19 21
|
| 40 |
+
CONECT 21 19 23 22
|
| 41 |
+
CONECT 22 21
|
| 42 |
+
CONECT 23 24 25 26 21
|
| 43 |
+
CONECT 24 23
|
| 44 |
+
CONECT 25 23
|
| 45 |
+
CONECT 26 23
|
| 46 |
+
END
|
grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/init_structures/gly_gly_grid_0208_0.pdb
ADDED
|
@@ -0,0 +1,46 @@
|
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|
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|
|
|
|
|
|
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|
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|
|
|
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|
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|
|
|
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|
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|
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|
|
|
|
|
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|
|
|
|
|
|
|
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|
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|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
REMARK 1 CREATED WITH MDTraj 1.10.3, 2026-03-03
|
| 2 |
+
CRYST1 21.865 21.865 21.865 90.00 90.00 90.00 P 1 1
|
| 3 |
+
MODEL 0
|
| 4 |
+
ATOM 1 H1 ACE A 1 21.100 12.600 17.950 1.00 0.00 H
|
| 5 |
+
ATOM 2 CH3 ACE A 1 21.170 11.710 17.320 1.00 0.00 C
|
| 6 |
+
ATOM 3 H2 ACE A 1 20.680 10.900 17.850 1.00 0.00 H
|
| 7 |
+
ATOM 4 H3 ACE A 1 22.220 11.420 17.210 1.00 0.00 H
|
| 8 |
+
ATOM 5 C ACE A 1 20.490 11.860 15.930 1.00 0.00 C
|
| 9 |
+
ATOM 6 O ACE A 1 19.850 12.880 15.660 1.00 0.00 O
|
| 10 |
+
ATOM 7 N GLY A 2 20.550 10.730 15.190 1.00 0.00 N
|
| 11 |
+
ATOM 8 H GLY A 2 21.010 9.960 15.660 1.00 0.00 H
|
| 12 |
+
ATOM 9 CA GLY A 2 19.450 10.460 14.250 1.00 0.00 C
|
| 13 |
+
ATOM 10 HA2 GLY A 2 18.500 10.800 14.670 1.00 0.00 H
|
| 14 |
+
ATOM 11 HA3 GLY A 2 19.730 10.830 13.270 1.00 0.00 H
|
| 15 |
+
ATOM 12 C GLY A 2 19.200 9.050 13.900 1.00 0.00 C
|
| 16 |
+
ATOM 13 O GLY A 2 18.060 8.620 13.560 1.00 0.00 O
|
| 17 |
+
ATOM 14 N GLY A 3 20.200 8.140 14.120 1.00 0.00 N
|
| 18 |
+
ATOM 15 H GLY A 3 20.900 8.470 14.760 1.00 0.00 H
|
| 19 |
+
ATOM 16 CA GLY A 3 19.980 6.680 14.000 1.00 0.00 C
|
| 20 |
+
ATOM 17 HA2 GLY A 3 19.530 6.610 13.010 1.00 0.00 H
|
| 21 |
+
ATOM 18 HA3 GLY A 3 20.950 6.180 13.920 1.00 0.00 H
|
| 22 |
+
ATOM 19 C GLY A 3 19.110 6.090 15.120 1.00 0.00 C
|
| 23 |
+
ATOM 20 O GLY A 3 18.320 6.760 15.860 1.00 0.00 O
|
| 24 |
+
ATOM 21 N NME A 4 19.310 4.760 15.320 1.00 0.00 N
|
| 25 |
+
ATOM 22 H NME A 4 19.920 4.260 14.690 1.00 0.00 H
|
| 26 |
+
ATOM 23 C NME A 4 18.720 3.990 16.430 1.00 0.00 C
|
| 27 |
+
ATOM 24 H1 NME A 4 17.750 4.410 16.680 1.00 0.00 H
|
| 28 |
+
ATOM 25 H2 NME A 4 18.540 2.970 16.100 1.00 0.00 H
|
| 29 |
+
ATOM 26 H3 NME A 4 19.380 4.080 17.300 1.00 0.00 H
|
| 30 |
+
TER 27 NME A 4
|
| 31 |
+
ENDMDL
|
| 32 |
+
CONECT 1 2
|
| 33 |
+
CONECT 2 5 1 3 4
|
| 34 |
+
CONECT 3 2
|
| 35 |
+
CONECT 4 2
|
| 36 |
+
CONECT 5 2 6 7
|
| 37 |
+
CONECT 6 5
|
| 38 |
+
CONECT 7 5
|
| 39 |
+
CONECT 19 21
|
| 40 |
+
CONECT 21 19 23 22
|
| 41 |
+
CONECT 22 21
|
| 42 |
+
CONECT 23 24 25 26 21
|
| 43 |
+
CONECT 24 23
|
| 44 |
+
CONECT 25 23
|
| 45 |
+
CONECT 26 23
|
| 46 |
+
END
|
grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/init_structures/gly_gly_grid_0210_0.pdb
ADDED
|
@@ -0,0 +1,46 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
REMARK 1 CREATED WITH MDTraj 1.10.3, 2026-03-03
|
| 2 |
+
CRYST1 21.911 21.911 21.911 90.00 90.00 90.00 P 1 1
|
| 3 |
+
MODEL 0
|
| 4 |
+
ATOM 1 H1 ACE A 1 15.310 0.310 14.540 1.00 0.00 H
|
| 5 |
+
ATOM 2 CH3 ACE A 1 15.370 0.960 13.660 1.00 0.00 C
|
| 6 |
+
ATOM 3 H2 ACE A 1 14.420 1.430 13.410 1.00 0.00 H
|
| 7 |
+
ATOM 4 H3 ACE A 1 15.550 0.340 12.790 1.00 0.00 H
|
| 8 |
+
ATOM 5 C ACE A 1 16.460 2.010 13.880 1.00 0.00 C
|
| 9 |
+
ATOM 6 O ACE A 1 17.530 1.560 14.290 1.00 0.00 O
|
| 10 |
+
ATOM 7 N GLY A 2 16.270 3.220 13.480 1.00 0.00 N
|
| 11 |
+
ATOM 8 H GLY A 2 15.360 3.350 13.060 1.00 0.00 H
|
| 12 |
+
ATOM 9 CA GLY A 2 17.180 4.330 13.570 1.00 0.00 C
|
| 13 |
+
ATOM 10 HA2 GLY A 2 17.740 4.400 14.500 1.00 0.00 H
|
| 14 |
+
ATOM 11 HA3 GLY A 2 17.950 4.310 12.800 1.00 0.00 H
|
| 15 |
+
ATOM 12 C GLY A 2 16.560 5.690 13.460 1.00 0.00 C
|
| 16 |
+
ATOM 13 O GLY A 2 17.110 6.690 13.890 1.00 0.00 O
|
| 17 |
+
ATOM 14 N GLY A 3 15.400 5.790 12.760 1.00 0.00 N
|
| 18 |
+
ATOM 15 H GLY A 3 15.050 5.000 12.240 1.00 0.00 H
|
| 19 |
+
ATOM 16 CA GLY A 3 14.740 7.070 12.670 1.00 0.00 C
|
| 20 |
+
ATOM 17 HA2 GLY A 3 15.430 7.840 12.300 1.00 0.00 H
|
| 21 |
+
ATOM 18 HA3 GLY A 3 14.000 7.150 11.870 1.00 0.00 H
|
| 22 |
+
ATOM 19 C GLY A 3 14.070 7.390 13.980 1.00 0.00 C
|
| 23 |
+
ATOM 20 O GLY A 3 14.370 8.450 14.490 1.00 0.00 O
|
| 24 |
+
ATOM 21 N NME A 4 13.120 6.600 14.410 1.00 0.00 N
|
| 25 |
+
ATOM 22 H NME A 4 13.080 5.710 13.940 1.00 0.00 H
|
| 26 |
+
ATOM 23 C NME A 4 12.290 6.840 15.640 1.00 0.00 C
|
| 27 |
+
ATOM 24 H1 NME A 4 12.680 6.340 16.530 1.00 0.00 H
|
| 28 |
+
ATOM 25 H2 NME A 4 12.250 7.890 15.940 1.00 0.00 H
|
| 29 |
+
ATOM 26 H3 NME A 4 11.290 6.490 15.410 1.00 0.00 H
|
| 30 |
+
TER 27 NME A 4
|
| 31 |
+
ENDMDL
|
| 32 |
+
CONECT 1 2
|
| 33 |
+
CONECT 2 5 1 3 4
|
| 34 |
+
CONECT 3 2
|
| 35 |
+
CONECT 4 2
|
| 36 |
+
CONECT 5 2 6 7
|
| 37 |
+
CONECT 6 5
|
| 38 |
+
CONECT 7 5
|
| 39 |
+
CONECT 19 21
|
| 40 |
+
CONECT 21 19 23 22
|
| 41 |
+
CONECT 22 21
|
| 42 |
+
CONECT 23 24 25 26 21
|
| 43 |
+
CONECT 24 23
|
| 44 |
+
CONECT 25 23
|
| 45 |
+
CONECT 26 23
|
| 46 |
+
END
|
grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/init_structures/gly_gly_grid_0215_0.pdb
ADDED
|
@@ -0,0 +1,46 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
REMARK 1 CREATED WITH MDTraj 1.10.3, 2026-03-03
|
| 2 |
+
CRYST1 21.916 21.916 21.916 90.00 90.00 90.00 P 1 1
|
| 3 |
+
MODEL 0
|
| 4 |
+
ATOM 1 H1 ACE A 1 8.390 -0.320 7.440 1.00 0.00 H
|
| 5 |
+
ATOM 2 CH3 ACE A 1 9.120 -0.420 8.250 1.00 0.00 C
|
| 6 |
+
ATOM 3 H2 ACE A 1 9.760 -1.280 8.080 1.00 0.00 H
|
| 7 |
+
ATOM 4 H3 ACE A 1 8.530 -0.700 9.120 1.00 0.00 H
|
| 8 |
+
ATOM 5 C ACE A 1 9.920 0.800 8.500 1.00 0.00 C
|
| 9 |
+
ATOM 6 O ACE A 1 9.290 1.790 8.960 1.00 0.00 O
|
| 10 |
+
ATOM 7 N GLY A 2 11.080 0.880 7.920 1.00 0.00 N
|
| 11 |
+
ATOM 8 H GLY A 2 11.500 0.010 7.650 1.00 0.00 H
|
| 12 |
+
ATOM 9 CA GLY A 2 11.890 2.080 7.730 1.00 0.00 C
|
| 13 |
+
ATOM 10 HA2 GLY A 2 11.290 2.960 7.530 1.00 0.00 H
|
| 14 |
+
ATOM 11 HA3 GLY A 2 12.330 2.190 8.720 1.00 0.00 H
|
| 15 |
+
ATOM 12 C GLY A 2 12.960 1.970 6.630 1.00 0.00 C
|
| 16 |
+
ATOM 13 O GLY A 2 13.320 3.000 6.040 1.00 0.00 O
|
| 17 |
+
ATOM 14 N GLY A 3 13.390 0.760 6.360 1.00 0.00 N
|
| 18 |
+
ATOM 15 H GLY A 3 12.890 -0.010 6.780 1.00 0.00 H
|
| 19 |
+
ATOM 16 CA GLY A 3 14.400 0.460 5.320 1.00 0.00 C
|
| 20 |
+
ATOM 17 HA2 GLY A 3 15.300 1.040 5.470 1.00 0.00 H
|
| 21 |
+
ATOM 18 HA3 GLY A 3 14.530 -0.620 5.410 1.00 0.00 H
|
| 22 |
+
ATOM 19 C GLY A 3 13.940 0.710 3.890 1.00 0.00 C
|
| 23 |
+
ATOM 20 O GLY A 3 12.740 0.860 3.530 1.00 0.00 O
|
| 24 |
+
ATOM 21 N NME A 4 14.940 0.950 3.050 1.00 0.00 N
|
| 25 |
+
ATOM 22 H NME A 4 15.870 1.050 3.440 1.00 0.00 H
|
| 26 |
+
ATOM 23 C NME A 4 14.740 1.140 1.640 1.00 0.00 C
|
| 27 |
+
ATOM 24 H1 NME A 4 14.550 0.150 1.230 1.00 0.00 H
|
| 28 |
+
ATOM 25 H2 NME A 4 13.940 1.850 1.460 1.00 0.00 H
|
| 29 |
+
ATOM 26 H3 NME A 4 15.660 1.550 1.230 1.00 0.00 H
|
| 30 |
+
TER 27 NME A 4
|
| 31 |
+
ENDMDL
|
| 32 |
+
CONECT 1 2
|
| 33 |
+
CONECT 2 5 1 3 4
|
| 34 |
+
CONECT 3 2
|
| 35 |
+
CONECT 4 2
|
| 36 |
+
CONECT 5 2 6 7
|
| 37 |
+
CONECT 6 5
|
| 38 |
+
CONECT 7 5
|
| 39 |
+
CONECT 19 21
|
| 40 |
+
CONECT 21 19 23 22
|
| 41 |
+
CONECT 22 21
|
| 42 |
+
CONECT 23 24 25 26 21
|
| 43 |
+
CONECT 24 23
|
| 44 |
+
CONECT 25 23
|
| 45 |
+
CONECT 26 23
|
| 46 |
+
END
|
grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/init_structures/gly_gly_grid_0232_0.pdb
ADDED
|
@@ -0,0 +1,46 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
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| 1 |
+
REMARK 1 CREATED WITH MDTraj 1.10.3, 2026-03-03
|
| 2 |
+
CRYST1 21.943 21.943 21.943 90.00 90.00 90.00 P 1 1
|
| 3 |
+
MODEL 0
|
| 4 |
+
ATOM 1 H1 ACE A 1 17.120 26.550 20.190 1.00 0.00 H
|
| 5 |
+
ATOM 2 CH3 ACE A 1 18.140 26.230 20.410 1.00 0.00 C
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| 6 |
+
ATOM 3 H2 ACE A 1 18.480 26.950 21.150 1.00 0.00 H
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| 7 |
+
ATOM 4 H3 ACE A 1 18.800 26.240 19.540 1.00 0.00 H
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| 8 |
+
ATOM 5 C ACE A 1 18.100 24.790 20.920 1.00 0.00 C
|
| 9 |
+
ATOM 6 O ACE A 1 18.690 24.470 21.940 1.00 0.00 O
|
| 10 |
+
ATOM 7 N GLY A 2 17.510 23.880 20.130 1.00 0.00 N
|
| 11 |
+
ATOM 8 H GLY A 2 17.220 24.190 19.220 1.00 0.00 H
|
| 12 |
+
ATOM 9 CA GLY A 2 17.340 22.460 20.500 1.00 0.00 C
|
| 13 |
+
ATOM 10 HA2 GLY A 2 18.210 22.210 21.110 1.00 0.00 H
|
| 14 |
+
ATOM 11 HA3 GLY A 2 16.430 22.340 21.100 1.00 0.00 H
|
| 15 |
+
ATOM 12 C GLY A 2 17.270 21.390 19.420 1.00 0.00 C
|
| 16 |
+
ATOM 13 O GLY A 2 17.610 20.290 19.670 1.00 0.00 O
|
| 17 |
+
ATOM 14 N GLY A 3 16.860 21.730 18.220 1.00 0.00 N
|
| 18 |
+
ATOM 15 H GLY A 3 16.270 22.550 18.220 1.00 0.00 H
|
| 19 |
+
ATOM 16 CA GLY A 3 16.590 20.740 17.150 1.00 0.00 C
|
| 20 |
+
ATOM 17 HA2 GLY A 3 16.530 21.200 16.160 1.00 0.00 H
|
| 21 |
+
ATOM 18 HA3 GLY A 3 17.390 20.010 17.060 1.00 0.00 H
|
| 22 |
+
ATOM 19 C GLY A 3 15.450 19.780 17.430 1.00 0.00 C
|
| 23 |
+
ATOM 20 O GLY A 3 14.550 20.210 18.170 1.00 0.00 O
|
| 24 |
+
ATOM 21 N NME A 4 15.420 18.600 16.800 1.00 0.00 N
|
| 25 |
+
ATOM 22 H NME A 4 16.280 18.340 16.340 1.00 0.00 H
|
| 26 |
+
ATOM 23 C NME A 4 14.230 17.670 16.700 1.00 0.00 C
|
| 27 |
+
ATOM 24 H1 NME A 4 14.220 17.090 17.620 1.00 0.00 H
|
| 28 |
+
ATOM 25 H2 NME A 4 13.290 18.200 16.580 1.00 0.00 H
|
| 29 |
+
ATOM 26 H3 NME A 4 14.300 17.080 15.790 1.00 0.00 H
|
| 30 |
+
TER 27 NME A 4
|
| 31 |
+
ENDMDL
|
| 32 |
+
CONECT 1 2
|
| 33 |
+
CONECT 2 5 1 3 4
|
| 34 |
+
CONECT 3 2
|
| 35 |
+
CONECT 4 2
|
| 36 |
+
CONECT 5 2 6 7
|
| 37 |
+
CONECT 6 5
|
| 38 |
+
CONECT 7 5
|
| 39 |
+
CONECT 19 21
|
| 40 |
+
CONECT 21 19 23 22
|
| 41 |
+
CONECT 22 21
|
| 42 |
+
CONECT 23 24 25 26 21
|
| 43 |
+
CONECT 24 23
|
| 44 |
+
CONECT 25 23
|
| 45 |
+
CONECT 26 23
|
| 46 |
+
END
|
grid_sampling/grid8_4d/runs/grid8_10ps_f1_20260303_065255/gly_gly/init_structures/gly_gly_grid_0235_0.pdb
ADDED
|
@@ -0,0 +1,46 @@
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|
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|
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|
|
|
|
|
|
|
| 1 |
+
REMARK 1 CREATED WITH MDTraj 1.10.3, 2026-03-03
|
| 2 |
+
CRYST1 21.817 21.817 21.817 90.00 90.00 90.00 P 1 1
|
| 3 |
+
MODEL 0
|
| 4 |
+
ATOM 1 H1 ACE A 1 10.410 5.240 5.290 1.00 0.00 H
|
| 5 |
+
ATOM 2 CH3 ACE A 1 10.220 4.860 4.290 1.00 0.00 C
|
| 6 |
+
ATOM 3 H2 ACE A 1 10.880 5.280 3.530 1.00 0.00 H
|
| 7 |
+
ATOM 4 H3 ACE A 1 9.200 5.070 3.970 1.00 0.00 H
|
| 8 |
+
ATOM 5 C ACE A 1 10.380 3.350 4.340 1.00 0.00 C
|
| 9 |
+
ATOM 6 O ACE A 1 11.340 2.920 4.970 1.00 0.00 O
|
| 10 |
+
ATOM 7 N GLY A 2 9.490 2.560 3.700 1.00 0.00 N
|
| 11 |
+
ATOM 8 H GLY A 2 8.650 3.030 3.390 1.00 0.00 H
|
| 12 |
+
ATOM 9 CA GLY A 2 9.680 1.110 3.360 1.00 0.00 C
|
| 13 |
+
ATOM 10 HA2 GLY A 2 10.630 0.850 2.910 1.00 0.00 H
|
| 14 |
+
ATOM 11 HA3 GLY A 2 9.610 0.560 4.300 1.00 0.00 H
|
| 15 |
+
ATOM 12 C GLY A 2 8.740 0.610 2.280 1.00 0.00 C
|
| 16 |
+
ATOM 13 O GLY A 2 9.030 -0.400 1.600 1.00 0.00 O
|
| 17 |
+
ATOM 14 N GLY A 3 7.580 1.220 2.230 1.00 0.00 N
|
| 18 |
+
ATOM 15 H GLY A 3 7.340 1.850 2.980 1.00 0.00 H
|
| 19 |
+
ATOM 16 CA GLY A 3 6.550 0.930 1.260 1.00 0.00 C
|
| 20 |
+
ATOM 17 HA2 GLY A 3 5.780 1.690 1.370 1.00 0.00 H
|
| 21 |
+
ATOM 18 HA3 GLY A 3 6.920 0.870 0.240 1.00 0.00 H
|
| 22 |
+
ATOM 19 C GLY A 3 5.780 -0.340 1.480 1.00 0.00 C
|
| 23 |
+
ATOM 20 O GLY A 3 4.550 -0.380 1.290 1.00 0.00 O
|
| 24 |
+
ATOM 21 N NME A 4 6.340 -1.240 2.250 1.00 0.00 N
|
| 25 |
+
ATOM 22 H NME A 4 7.340 -1.270 2.390 1.00 0.00 H
|
| 26 |
+
ATOM 23 C NME A 4 5.690 -2.360 2.920 1.00 0.00 C
|
| 27 |
+
ATOM 24 H1 NME A 4 5.320 -1.940 3.850 1.00 0.00 H
|
| 28 |
+
ATOM 25 H2 NME A 4 4.840 -2.680 2.330 1.00 0.00 H
|
| 29 |
+
ATOM 26 H3 NME A 4 6.400 -3.190 3.040 1.00 0.00 H
|
| 30 |
+
TER 27 NME A 4
|
| 31 |
+
ENDMDL
|
| 32 |
+
CONECT 1 2
|
| 33 |
+
CONECT 2 5 1 3 4
|
| 34 |
+
CONECT 3 2
|
| 35 |
+
CONECT 4 2
|
| 36 |
+
CONECT 5 2 6 7
|
| 37 |
+
CONECT 6 5
|
| 38 |
+
CONECT 7 5
|
| 39 |
+
CONECT 19 21
|
| 40 |
+
CONECT 21 19 23 22
|
| 41 |
+
CONECT 22 21
|
| 42 |
+
CONECT 23 24 25 26 21
|
| 43 |
+
CONECT 24 23
|
| 44 |
+
CONECT 25 23
|
| 45 |
+
CONECT 26 23
|
| 46 |
+
END
|