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pnovelli commited on
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Delete G3

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Files changed (19) hide show
  1. G3/data/NVT.mdp +0 -70
  2. G3/data/b.gro +0 -0
  3. G3/data/com.ndx +0 -0
  4. G3/data/conf_template.pdb +0 -41
  5. G3/data/md.tpr +0 -3
  6. G3/data/no_water.gro +0 -231
  7. G3/data/plumed.dat +0 -19
  8. G3/data/run.sh +0 -16
  9. G3/data/u.gro +0 -0
  10. G3/traj/traj_com_0.trr +0 -3
  11. G3/traj/traj_com_1.trr +0 -3
  12. G3/traj/traj_com_2.trr +0 -3
  13. G3/traj/traj_com_3.trr +0 -3
  14. G3/traj/traj_com_4.trr +0 -3
  15. G3/traj/traj_com_5.trr +0 -3
  16. G3/traj/traj_com_6.trr +0 -3
  17. G3/traj/traj_com_7.trr +0 -3
  18. G3/traj/traj_com_8.trr +0 -3
  19. G3/traj/traj_com_9.trr +0 -3
G3/data/NVT.mdp DELETED
@@ -1,70 +0,0 @@
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- define =
2
-
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- ; Integrator stuff
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- integrator = md ; steep or md
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- dt = 0.002
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- nsteps = 250000000 ; -1 no maximum
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- init-step = 0 ;
8
- continuation = no
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-
10
- ; neighbour search
11
- cutoff-scheme = verlet ; the other is bad
12
- nst-list = 10 ;frequency of update of neighbours, with verlet-buf-tol its a minimum
13
- verlet-buffer-tolerance = 0.005 ; kj/mol/ps might need to put -1.
14
- ns-type = grid
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-
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-
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- ; Pbc
18
- pbc = xyz ; xyz or xy
19
-
20
- ; Vdw
21
- rvdw = 1.0
22
- vdwtype = cut-off ; PME or User to look for table /user
23
- DispCorr = EnerPres ; corrections to energy and pressure or No
24
-
25
- ;Electrostatic
26
- coulombtype = PME ; User if look for table
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- rcoulomb = 1.0
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- pme-order = 4
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- fourierspacing = 0.1
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- ewald-rtol = 1.e-5 ; splitting between real and reciprocal
31
- ewald-geometry = 3d ; 3d or 3dc
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-
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- IMD-group = non-Water
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-
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- ; T and P
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- tcoupl = v-rescale ; none, nose-hoover, v-rescale
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- nsttcouple = 10 ; 10 if not used
38
- tc-grps = OCB MOL Water_and_ions
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- tau-t = 0.1 0.1 0.1 ; ps
40
- ref-t = 300 300 300 ; K
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- pcoupl = no ;
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- pcoupltype = isotropic ;
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- compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1
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- refcoord-scaling = com
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- tau-p = 5.0 ; ps
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- ref-p = 1.0 ; bar
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-
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- ; Constraints
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- constraints = all-bonds ; constraints distances
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- constraint-algorithm = LINCS ; or SHAKE
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- lincs_iter = 1
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- lincs_order = 4
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-
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- ;Generate velocities
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- gen_vel = yes ; assign velocities from Maxwell distribution
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- gen_temp = 300 ; temperature for Maxwell distribution
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- gen_seed = -1 ; generate a random seed
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-
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-
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- ; OUTPUT
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- ; Output control
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- nstenergy = 1000 ; save energies
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- nstlog = 1000 ; update log file every
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- nstxout = 500 ; save coordinates every 1.0 ps
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- ; nstxout-compressed replaces nstxtcout
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-
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- ; COM removal . There are more options like removing from groups or the frequency
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- comm-mode = linear ; linear, angular (removes linear and angular motion) or none
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- nstcomm = 100 ; frequency of removal of com motion
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- nstcalcenergy = 500
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
G3/data/b.gro DELETED
The diff for this file is too large to render. See raw diff
 
G3/data/com.ndx DELETED
The diff for this file is too large to render. See raw diff
 
G3/data/conf_template.pdb DELETED
@@ -1,41 +0,0 @@
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- ATOM 33 C1 OCB B 2 18.896 23.137 19.226 1.00 1.00 C
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- ATOM 34 C2 OCB B 2 21.342 23.951 20.381 1.00 1.00 C
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- ATOM 35 C3 OCB X 2 20.136 22.782 18.629 1.00 1.00 C
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- ATOM 36 C4 OCB X 2 18.931 23.951 20.381 1.00 1.00 C
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- ATOM 37 C5 OCB X 2 20.136 24.324 20.962 1.00 1.00 C
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- ATOM 38 C6 OCB X 2 21.377 23.137 19.226 1.00 1.00 C
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- ATOM 39 O1 OCB X 2 22.507 24.274 21.064 1.00 1.00 O
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- ATOM 40 C7 OCB X 2 22.744 22.744 18.579 1.00 1.00 C
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- ATOM 41 C8 OCB X 2 23.163 23.163 21.851 1.00 1.00 C
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- ATOM 42 O2 OCB X 2 24.274 22.507 21.064 1.00 1.00 O
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- ATOM 43 C9 OCB X 2 23.951 21.342 20.381 1.00 1.00 C
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- ATOM 44 C10 OCB X 2 23.137 21.377 19.226 1.00 1.00 C
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- ATOM 45 C11 OCB X 2 22.782 20.136 18.629 1.00 1.00 C
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- ATOM 46 C12 OCB X 2 24.324 20.136 20.962 1.00 1.00 C
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- ATOM 47 C13 OCB X 2 23.137 18.896 19.226 1.00 1.00 C
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- ATOM 48 C14 OCB X 2 23.951 18.931 20.381 1.00 1.00 C
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- ATOM 49 O3 OCB X 2 24.274 17.765 21.064 1.00 1.00 O
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- ATOM 50 C15 OCB X 2 22.744 17.528 18.579 1.00 1.00 C
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- ATOM 51 C16 OCB X 2 21.377 17.135 19.226 1.00 1.00 C
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- ATOM 52 C17 OCB X 2 21.342 16.321 20.381 1.00 1.00 C
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- ATOM 53 C18 OCB X 2 23.163 17.109 21.851 1.00 1.00 C
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- ATOM 54 O4 OCB X 2 22.507 15.998 21.064 1.00 1.00 O
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- ATOM 55 O5 OCB X 2 17.765 24.274 21.064 1.00 1.00 O
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- ATOM 56 C19 OCB X 2 17.528 22.744 18.579 1.00 1.00 C
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- ATOM 57 C20 OCB X 2 17.135 21.377 19.226 1.00 1.00 C
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- ATOM 58 O6 OCB X 2 15.998 22.507 21.064 1.00 1.00 O
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- ATOM 59 C21 OCB X 2 16.321 21.342 20.381 1.00 1.00 C
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- ATOM 60 C22 OCB X 2 20.136 15.948 20.962 1.00 1.00 C
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- ATOM 61 C23 OCB X 2 18.931 16.321 20.381 1.00 1.00 C
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- ATOM 62 C24 OCB X 2 15.948 20.136 20.962 1.00 1.00 C
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- ATOM 63 C25 OCB X 2 16.321 18.931 20.381 1.00 1.00 C
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- ATOM 64 O7 OCB X 2 17.765 15.998 21.064 1.00 1.00 O
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- ATOM 65 O8 OCB X 2 15.998 17.765 21.064 1.00 1.00 O
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- ATOM 66 C26 OCB X 2 17.109 17.109 21.851 1.00 1.00 C
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- ATOM 67 C27 OCB X 2 17.490 20.136 18.629 1.00 1.00 C
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- ATOM 68 C28 OCB X 2 17.135 18.896 19.226 1.00 1.00 C
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- ATOM 69 C29 OCB X 2 20.136 17.490 18.629 1.00 1.00 C
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- ATOM 70 C30 OCB X 2 17.528 17.528 18.579 1.00 1.00 C
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- ATOM 71 C31 OCB X 2 18.896 17.135 19.226 1.00 1.00 C
40
- ATOM 72 C32 OCB X 2 17.109 23.163 21.851 1.00 1.00 C
41
- END
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
G3/data/md.tpr DELETED
@@ -1,3 +0,0 @@
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- version https://git-lfs.github.com/spec/v1
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- oid sha256:cda1e9466f9287fe08e2e1daf25f0a5126abde9ed94ddb8e0973dd8a86a794a0
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- size 227812
 
 
 
 
G3/data/no_water.gro DELETED
@@ -1,231 +0,0 @@
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- Generic title t= 12112.00000 step= 6056000
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- 228
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- 1MOL C1 1 1.315 3.873 2.237
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- 1MOL C2 2 1.339 3.725 2.271
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- 1MOL C3 3 1.309 3.624 2.160
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- 1MOL C4 4 1.409 3.635 2.044
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- 1MOL C5 5 1.379 3.534 1.932
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- 1MOL C6 6 1.416 3.392 1.977
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- 1MOL N1 7 1.399 3.285 1.873
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- 1MOL C7 8 1.399 3.145 1.927
11
- 1MOL C8 9 1.503 3.303 1.767
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- 1MOL C9 10 1.267 3.316 1.810
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- 1MOL H1 11 1.252 3.871 2.148
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- 1MOL H2 12 1.260 3.919 2.318
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- 1MOL H3 13 1.273 3.709 2.357
16
- 1MOL H4 14 1.442 3.731 2.307
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- 1MOL H5 15 1.206 3.635 2.127
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- 1MOL H6 16 1.310 3.522 2.199
19
- 1MOL H7 17 1.510 3.627 2.084
20
- 1MOL H8 18 1.399 3.736 2.005
21
- 1MOL H9 19 1.440 3.566 1.847
22
- 1MOL H10 20 1.274 3.538 1.904
23
- 1MOL H11 21 1.357 3.356 2.061
24
- 1MOL H12 22 1.522 3.392 2.004
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- 1MOL H13 23 1.408 3.925 2.210
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- 1MOL H14 24 1.304 3.125 1.976
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- 1MOL H15 25 1.413 3.080 1.840
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- 1MOL H16 26 1.483 3.126 1.994
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- 1MOL H17 27 1.490 3.219 1.698
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- 1MOL H18 28 1.471 3.392 1.712
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- 1MOL H19 29 1.603 3.295 1.809
32
- 1MOL H20 30 1.228 3.226 1.762
33
- 1MOL H21 31 1.190 3.332 1.886
34
- 1MOL H22 32 1.268 3.407 1.750
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- 2OCB C1 33 2.395 0.048 3.524
36
- 2OCB C2 34 2.540 4.024 3.295
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- 2OCB C3 35 2.491 0.136 3.477
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- 2OCB C4 36 2.365 3.970 3.444
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- 2OCB C5 37 2.436 3.939 3.329
40
- 2OCB C6 38 2.566 0.110 3.363
41
- 2OCB O1 39 2.601 4.002 3.174
42
- 2OCB C7 40 2.671 0.208 3.315
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- 2OCB C8 41 2.559 0.045 3.059
44
- 2OCB O2 42 2.640 0.161 3.033
45
- 2OCB C9 43 2.599 0.280 3.088
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- 2OCB C10 44 2.606 0.309 3.223
47
- 2OCB C11 45 2.548 0.424 3.274
48
- 2OCB C12 46 2.545 0.371 2.998
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- 2OCB C13 47 2.497 0.521 3.189
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- 2OCB C14 48 2.491 0.486 3.055
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- 2OCB O3 49 2.416 0.568 2.974
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- 2OCB C15 50 2.435 0.648 3.244
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- 2OCB C16 51 2.294 0.621 3.291
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- 2OCB C17 52 2.193 0.638 3.197
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- 2OCB C18 53 2.273 0.554 2.983
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- 2OCB O4 54 2.225 0.662 3.065
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- 2OCB O5 55 2.256 3.895 3.479
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- 2OCB C19 56 2.319 0.082 3.651
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- 2OCB C20 57 2.198 0.167 3.623
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- 2OCB O6 58 2.077 4.001 3.578
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- 2OCB C21 59 2.076 0.103 3.603
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- 2OCB C22 60 2.061 0.619 3.233
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- 2OCB C23 61 2.028 0.588 3.364
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- 2OCB C24 62 1.962 0.177 3.575
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- 2OCB C25 63 1.971 0.315 3.577
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- 2OCB O7 64 1.896 0.558 3.391
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- 2OCB O8 65 1.859 0.382 3.535
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- 2OCB C26 66 1.860 0.419 3.396
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- 2OCB C27 67 2.200 0.304 3.641
70
- 2OCB C28 68 2.087 0.381 3.616
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- 2OCB C29 69 2.257 0.580 3.418
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- 2OCB C30 70 2.094 0.532 3.604
73
- 2OCB C31 71 2.125 0.566 3.460
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- 2OCB C32 72 2.131 3.960 3.451
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- 2OCB C33 73 2.536 0.709 3.342
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- 2OCB C34 74 2.509 0.857 3.372
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- 2OCB C35 75 2.604 0.935 3.459
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- 2OCB O9 76 2.570 0.960 3.573
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- 2OCB C36 77 2.757 0.277 3.422
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- 2OCB C37 78 2.865 0.182 3.473
81
- 2OCB C38 79 2.916 0.239 3.603
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- 2OCB O10 80 3.033 0.219 3.627
83
- 2OCB C39 81 2.413 0.128 3.763
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- 2OCB C40 82 2.352 0.141 3.903
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- 2OCB C41 83 2.465 0.170 3.999
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- 2OCB O11 84 2.471 0.088 0.055
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- 2OCB C42 85 2.175 0.603 3.713
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- 2OCB C43 86 2.124 0.599 3.857
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- 2OCB C44 87 1.994 0.674 3.864
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- 2OCB O12 88 1.892 0.613 3.891
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- 2OCB C45 89 2.535 3.990 2.937
92
- 2OCB C46 90 2.458 3.837 2.714
93
- 2OCB C47 91 2.525 0.014 2.811
94
- 2OCB C48 92 2.496 3.858 2.953
95
- 2OCB C49 93 2.462 3.783 2.842
96
- 2OCB C50 94 2.498 3.969 2.699
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- 2OCB C51 95 2.026 3.870 3.389
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- 2OCB C52 96 1.859 3.683 3.272
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- 2OCB C53 97 1.891 3.869 3.422
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- 2OCB C54 98 2.072 3.792 3.284
101
- 2OCB C55 99 1.989 3.697 3.226
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- 2OCB C56 100 1.811 3.768 3.370
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- 2OCB C57 101 1.731 0.387 3.325
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- 2OCB C58 102 1.522 0.302 3.173
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- 2OCB C59 103 1.712 0.444 3.200
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- 2OCB C60 104 1.649 0.286 3.374
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- 2OCB C61 105 1.543 0.242 3.296
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- 2OCB C62 106 1.607 0.398 3.121
109
- 2OCB C63 107 2.212 0.547 2.846
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- 2OCB C64 108 2.072 0.526 2.599
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- 2OCB C65 109 2.083 0.597 2.828
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- 2OCB C66 110 2.268 0.483 2.736
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- 2OCB C67 111 2.196 0.465 2.619
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- 2OCB C68 112 2.017 0.593 2.707
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- 2OCB O13 113 2.034 3.606 3.134
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- 2OCB O14 114 1.456 0.142 3.331
117
- 2OCB O15 115 1.572 0.451 2.999
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- 2OCB O16 116 2.417 3.654 2.853
119
- 2OCB O17 117 2.499 4.019 2.571
120
- 2OCB O18 118 1.891 0.647 2.697
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- 2OCB O19 119 2.245 0.392 2.513
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- 2OCB C69 120 1.487 0.035 3.411
123
- 2OCB C70 121 1.581 3.871 3.581
124
- 2OCB C71 122 1.558 3.959 3.359
125
- 2OCB C72 123 1.463 0.044 3.547
126
- 2OCB C73 124 1.505 3.975 3.632
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- 2OCB C74 125 1.600 3.859 3.444
128
- 2OCB O20 126 1.678 3.754 3.402
129
- 2OCB C75 127 2.359 3.607 2.969
130
- 2OCB C76 128 2.244 3.526 3.209
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- 2OCB C77 129 2.432 3.538 3.065
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- 2OCB C78 130 2.226 3.634 2.993
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- 2OCB C79 131 2.168 3.589 3.111
134
- 2OCB C80 132 2.375 3.491 3.182
135
- 2OCB C81 133 1.632 0.560 2.941
136
- 2OCB C82 134 1.723 0.774 2.791
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- 2OCB C83 135 1.573 0.684 2.955
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- 2OCB C84 136 1.743 0.542 2.860
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- 2OCB C85 137 1.790 0.652 2.790
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- 2OCB C86 138 1.616 0.791 2.877
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- 2OCB C87 139 1.530 0.912 2.881
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- 2OCB O21 140 1.564 1.015 2.828
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- 2OCB C88 141 2.723 0.378 2.398
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- 2OCB O22 142 2.825 0.312 2.399
145
- 2OCB C89 143 2.450 3.411 3.283
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- 2OCB O23 144 2.392 3.335 3.359
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- 2OCB O24 145 2.711 0.971 3.414
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- 2OCB O25 146 1.988 0.792 3.836
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- 2OCB O26 147 2.523 0.277 3.996
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- 2OCB C90 148 1.479 3.976 3.778
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- 2OCB O27 149 1.444 0.042 3.840
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- 2OCB O28 150 2.721 0.495 2.365
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- 2OCB O30 152 1.492 3.875 3.844
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- 2OCB C92 156 2.480 0.383 2.470
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161
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166
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169
- 2OCB H3 167 2.738 0.146 3.256
170
- 2OCB H4 168 2.460 0.082 3.088
171
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174
- 2OCB H8 172 2.239 0.462 3.033
175
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176
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177
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178
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179
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180
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181
- 2OCB H15 179 1.997 0.579 3.617
182
- 2OCB H16 180 2.143 0.014 3.384
183
- 2OCB H17 181 2.532 0.657 3.437
184
- 2OCB H18 182 2.640 0.702 3.310
185
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186
- 2OCB H20 184 2.408 0.858 3.415
187
- 2OCB H21 185 2.700 0.312 3.508
188
- 2OCB H22 186 2.809 0.367 3.389
189
- 2OCB H23 187 2.826 0.081 3.488
190
- 2OCB H24 188 2.943 0.166 3.399
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- 2OCB H25 189 2.493 0.052 3.761
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- 2OCB H26 190 2.467 0.218 3.735
193
- 2OCB H27 191 2.279 0.222 3.903
194
- 2OCB H28 192 2.292 0.060 3.944
195
- 2OCB H29 193 2.278 0.565 3.721
196
- 2OCB H30 194 2.177 0.709 3.688
197
- 2OCB H31 195 2.098 0.497 3.885
198
- 2OCB H32 196 2.197 0.641 3.927
199
- 2OCB H33 197 2.414 3.777 2.635
200
- 2OCB H34 198 2.560 0.117 2.799
201
- 2OCB H35 199 2.505 3.808 3.049
202
- 2OCB H36 200 1.799 3.599 3.238
203
- 2OCB H37 201 1.858 3.917 3.513
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- 2OCB H38 202 2.177 3.789 3.255
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- 2OCB H39 203 1.435 0.275 3.113
206
- 2OCB H40 204 1.772 0.524 3.157
207
- 2OCB H41 205 1.678 0.236 3.466
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- 2OCB H42 206 2.024 0.523 2.502
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- 2OCB H43 207 2.033 0.629 2.919
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- 2OCB H44 208 2.364 0.436 2.750
211
- 2OCB H45 209 1.621 3.798 3.651
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- 2OCB H46 210 1.415 0.136 3.582
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- 2OCB H47 211 2.197 3.495 3.302
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- 2OCB H48 212 2.535 3.515 3.041
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- 2OCB H49 213 1.749 0.852 2.720
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- 2OCB H50 214 1.490 0.690 3.026
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- 2OCB H51 215 2.484 0.489 2.448
218
- 2OCB H52 216 2.703 0.141 2.522
219
- 2OCB H53 217 2.168 0.141 2.515
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- 2OCB H54 218 2.252 0.010 2.590
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- 2OCB H55 219 2.210 0.141 2.694
222
- 2OCB H56 220 2.153 3.822 2.964
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- 2OCB H57 221 2.175 3.745 2.806
224
- 2OCB H58 222 2.035 3.705 2.899
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- 2OCB H59 223 1.517 4.009 3.152
226
- 2OCB H60 224 1.687 3.986 3.192
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- 2OCB H61 225 1.572 3.844 3.182
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- 2OCB H62 226 1.860 0.402 2.761
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- 2OCB H63 227 1.861 0.371 2.935
230
- 2OCB H64 228 1.711 0.337 2.834
231
- 4.03223 4.03223 4.03223
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
G3/data/plumed.dat DELETED
@@ -1,19 +0,0 @@
1
- HOST: GROUP ATOMS=33-228 #host atoms
2
- LIGC: GROUP ATOMS=1-6,8-10 #carbon atoms in the ligand
3
-
4
- WHOLEMOLECULES ENTITY0=HOST
5
- FIT_TO_TEMPLATE STRIDE=1 REFERENCE=conf_template.pdb TYPE=OPTIMAL #coordinates alignment
6
- lig: CENTER ATOMS=LIGC
7
-
8
- v1: FIXEDATOM AT=2.0136,2.0136,2.0 #virtual atoms
9
-
10
- cyl: DISTANCE ATOMS=v1,lig COMPONENTS
11
- radius: MATHEVAL ARG=cyl.x,cyl.y FUNC=sqrt(x*x+y*y) PERIODIC=NO
12
-
13
- funnel: MATHEVAL ARG=radius,cyl.z VAR=r,z FUNC=(r+1.0*(-1.2+z))*step(-z+1.)+(r-0.2)*step(z-1.) PERIODIC=NO
14
- UPPER_WALLS AT=0 ARG=funnel KAPPA=2000.0 LABEL=funnelwall #funnel restraint
15
- UPPER_WALLS AT=1.8 ARG=cyl.z KAPPA=4000.0 EXP=2 LABEL=upper_wall #upper limit of cyl.z
16
-
17
- PRINT ARG=* STRIDE=250 FILE=COLVAR FMT=%8.4f
18
-
19
- ENDPLUMED
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
G3/data/run.sh DELETED
@@ -1,16 +0,0 @@
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- #!/bin/bash
2
- #SBATCH -J G3
3
- #SBATCH -o G3.log
4
- #SBATCH -e G3.err
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- #SBATCH -N 1
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- #SBATCH -p gpu
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- #SBATCH --gres=gpu:1
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- #SBATCH --cpus-per-task=1
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- #SBATCH --ntasks=4
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- ##SBATCH -w gpu05
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-
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- module load cuda/11.8
13
- newdir=./
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- nsteps=500000000 # 1us
15
- gmx_mpi mdrun -plumed plumed.dat -nsteps $nsteps -s md.tpr
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-
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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