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- .gitattributes +39 -0
- calixarene/G1/data/NVT.mdp +70 -0
- calixarene/G1/data/com.ndx +0 -0
- calixarene/G1/data/conf_template.pdb +41 -0
- calixarene/G1/data/md.tpr +3 -0
- calixarene/G1/data/no_water.gro +214 -0
- calixarene/G1/data/plumed.dat +19 -0
- calixarene/G1/data/u.gro +0 -0
- calixarene/G1/traj/traj_com_0.trr +3 -0
- calixarene/G1/traj/traj_com_1.trr +3 -0
- calixarene/G1/traj/traj_com_10.trr +3 -0
- calixarene/G1/traj/traj_com_11.trr +3 -0
- calixarene/G1/traj/traj_com_12.trr +3 -0
- calixarene/G1/traj/traj_com_13.trr +3 -0
- calixarene/G1/traj/traj_com_14.trr +3 -0
- calixarene/G1/traj/traj_com_15.trr +3 -0
- calixarene/G1/traj/traj_com_2.trr +3 -0
- calixarene/G1/traj/traj_com_3.trr +3 -0
- calixarene/G1/traj/traj_com_4.trr +3 -0
- calixarene/G1/traj/traj_com_5.trr +3 -0
- calixarene/G1/traj/traj_com_6.trr +3 -0
- calixarene/G1/traj/traj_com_7.trr +3 -0
- calixarene/G1/traj/traj_com_8.trr +3 -0
- calixarene/G1/traj/traj_com_9.trr +3 -0
- calixarene/G2/data/NVT.mdp +70 -0
- calixarene/G2/data/com.ndx +0 -0
- calixarene/G2/data/conf_template.pdb +41 -0
- calixarene/G2/data/md.tpr +3 -0
- calixarene/G2/data/no_water.gro +214 -0
- calixarene/G2/data/plumed.dat +19 -0
- calixarene/G2/data/topol.top +0 -0
- calixarene/G2/data/u.gro +0 -0
- calixarene/G2/traj/traj_com_0.trr +3 -0
- calixarene/G2/traj/traj_com_1.trr +3 -0
- calixarene/G2/traj/traj_com_2.trr +3 -0
- calixarene/G2/traj/traj_com_3.trr +3 -0
- calixarene/G2/traj/traj_com_4.trr +3 -0
- calixarene/G2/traj/traj_com_5.trr +3 -0
- calixarene/G2/traj/traj_com_6.trr +3 -0
- calixarene/G2/traj/traj_com_7.trr +3 -0
- calixarene/G2/traj/traj_com_8.trr +3 -0
- calixarene/G2/traj/traj_com_9.trr +3 -0
- calixarene/G3/data/NVT.mdp +70 -0
- calixarene/G3/data/b.gro +0 -0
- calixarene/G3/data/com.ndx +0 -0
- calixarene/G3/data/conf_template.pdb +41 -0
- calixarene/G3/data/md.tpr +3 -0
- calixarene/G3/data/no_water.gro +231 -0
- calixarene/G3/data/plumed.dat +19 -0
- calixarene/G3/data/run.sh +16 -0
.gitattributes
CHANGED
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@@ -98,3 +98,42 @@ G3/traj/traj_com_6.trr filter=lfs diff=lfs merge=lfs -text
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G3/traj/traj_com_7.trr filter=lfs diff=lfs merge=lfs -text
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G3/traj/traj_com_8.trr filter=lfs diff=lfs merge=lfs -text
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G3/traj/traj_com_9.trr filter=lfs diff=lfs merge=lfs -text
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G3/traj/traj_com_7.trr filter=lfs diff=lfs merge=lfs -text
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G3/traj/traj_com_8.trr filter=lfs diff=lfs merge=lfs -text
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G3/traj/traj_com_9.trr filter=lfs diff=lfs merge=lfs -text
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calixarene/G1/data/md.tpr filter=lfs diff=lfs merge=lfs -text
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calixarene/G1/traj/traj_com_0.trr filter=lfs diff=lfs merge=lfs -text
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calixarene/G1/traj/traj_com_1.trr filter=lfs diff=lfs merge=lfs -text
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calixarene/G1/traj/traj_com_10.trr filter=lfs diff=lfs merge=lfs -text
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calixarene/G1/traj/traj_com_11.trr filter=lfs diff=lfs merge=lfs -text
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calixarene/G1/traj/traj_com_12.trr filter=lfs diff=lfs merge=lfs -text
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calixarene/G1/traj/traj_com_13.trr filter=lfs diff=lfs merge=lfs -text
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calixarene/G1/traj/traj_com_14.trr filter=lfs diff=lfs merge=lfs -text
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calixarene/G1/traj/traj_com_15.trr filter=lfs diff=lfs merge=lfs -text
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calixarene/G1/traj/traj_com_2.trr filter=lfs diff=lfs merge=lfs -text
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calixarene/G1/traj/traj_com_3.trr filter=lfs diff=lfs merge=lfs -text
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calixarene/G1/traj/traj_com_4.trr filter=lfs diff=lfs merge=lfs -text
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calixarene/G1/traj/traj_com_5.trr filter=lfs diff=lfs merge=lfs -text
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calixarene/G1/traj/traj_com_6.trr filter=lfs diff=lfs merge=lfs -text
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calixarene/G1/traj/traj_com_7.trr filter=lfs diff=lfs merge=lfs -text
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calixarene/G1/traj/traj_com_8.trr filter=lfs diff=lfs merge=lfs -text
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calixarene/G1/traj/traj_com_9.trr filter=lfs diff=lfs merge=lfs -text
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calixarene/G2/data/md.tpr filter=lfs diff=lfs merge=lfs -text
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calixarene/G2/traj/traj_com_0.trr filter=lfs diff=lfs merge=lfs -text
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calixarene/G2/traj/traj_com_1.trr filter=lfs diff=lfs merge=lfs -text
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calixarene/G2/traj/traj_com_2.trr filter=lfs diff=lfs merge=lfs -text
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calixarene/G2/traj/traj_com_3.trr filter=lfs diff=lfs merge=lfs -text
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calixarene/G2/traj/traj_com_4.trr filter=lfs diff=lfs merge=lfs -text
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calixarene/G2/traj/traj_com_5.trr filter=lfs diff=lfs merge=lfs -text
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calixarene/G2/traj/traj_com_6.trr filter=lfs diff=lfs merge=lfs -text
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calixarene/G2/traj/traj_com_7.trr filter=lfs diff=lfs merge=lfs -text
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calixarene/G2/traj/traj_com_8.trr filter=lfs diff=lfs merge=lfs -text
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calixarene/G2/traj/traj_com_9.trr filter=lfs diff=lfs merge=lfs -text
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calixarene/G3/data/md.tpr filter=lfs diff=lfs merge=lfs -text
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calixarene/G3/traj/traj_com_0.trr filter=lfs diff=lfs merge=lfs -text
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calixarene/G3/traj/traj_com_1.trr filter=lfs diff=lfs merge=lfs -text
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calixarene/G3/traj/traj_com_2.trr filter=lfs diff=lfs merge=lfs -text
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calixarene/G3/traj/traj_com_3.trr filter=lfs diff=lfs merge=lfs -text
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calixarene/G3/traj/traj_com_4.trr filter=lfs diff=lfs merge=lfs -text
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calixarene/G3/traj/traj_com_5.trr filter=lfs diff=lfs merge=lfs -text
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calixarene/G3/traj/traj_com_6.trr filter=lfs diff=lfs merge=lfs -text
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calixarene/G3/traj/traj_com_7.trr filter=lfs diff=lfs merge=lfs -text
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calixarene/G3/traj/traj_com_8.trr filter=lfs diff=lfs merge=lfs -text
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calixarene/G3/traj/traj_com_9.trr filter=lfs diff=lfs merge=lfs -text
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calixarene/G1/data/NVT.mdp
ADDED
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| 1 |
+
define =
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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 ;
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continuation = no
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; neighbour search
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cutoff-scheme = verlet ; the other is bad
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nst-list = 10 ;frequency of update of neighbours, with verlet-buf-tol its a minimum
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verlet-buffer-tolerance = 0.005 ; kj/mol/ps might need to put -1.
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ns-type = grid
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; Pbc
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pbc = xyz ; xyz or xy
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; Vdw
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rvdw = 1.0
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vdwtype = cut-off ; PME or User to look for table /user
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DispCorr = EnerPres ; corrections to energy and pressure or No
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;Electrostatic
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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
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ewald-geometry = 3d ; 3d or 3dc
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IMD-group = non-Water
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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
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tc-grps = OCB MOL Water_and_ions
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tau-t = 0.1 0.1 0.1 ; ps
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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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; Constraints
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| 49 |
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constraints = all-bonds ; constraints distances
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| 50 |
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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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;Generate velocities
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| 55 |
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gen_vel = yes ; assign velocities from Maxwell distribution
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| 56 |
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gen_temp = 300 ; temperature for Maxwell distribution
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| 57 |
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gen_seed = -1 ; generate a random seed
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| 58 |
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| 59 |
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| 60 |
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; OUTPUT
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| 61 |
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; Output control
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| 62 |
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nstenergy = 1000 ; save energies
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| 63 |
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nstlog = 1000 ; update log file every
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| 64 |
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nstxout = 500 ; save coordinates every 1.0 ps
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| 65 |
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; nstxout-compressed replaces nstxtcout
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| 66 |
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| 67 |
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; COM removal . There are more options like removing from groups or the frequency
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| 68 |
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comm-mode = linear ; linear, angular (removes linear and angular motion) or none
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| 69 |
+
nstcomm = 100 ; frequency of removal of com motion
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| 70 |
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nstcalcenergy = 500
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calixarene/G1/data/com.ndx
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The diff for this file is too large to render.
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calixarene/G1/data/conf_template.pdb
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| 1 |
+
ATOM 16 C1 OCB B 2 18.896 23.137 19.226 1.00 1.00 C
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ATOM 17 C2 OCB B 2 21.342 23.951 20.381 1.00 1.00 C
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| 3 |
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ATOM 18 C3 OCB X 2 20.136 22.782 18.629 1.00 1.00 C
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ATOM 19 C4 OCB X 2 18.931 23.951 20.381 1.00 1.00 C
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ATOM 20 C5 OCB X 2 20.136 24.324 20.962 1.00 1.00 C
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ATOM 21 C6 OCB X 2 21.377 23.137 19.226 1.00 1.00 C
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ATOM 22 O1 OCB X 2 22.507 24.274 21.064 1.00 1.00 O
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| 8 |
+
ATOM 23 C7 OCB X 2 22.744 22.744 18.579 1.00 1.00 C
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| 9 |
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ATOM 24 C8 OCB X 2 23.163 23.163 21.851 1.00 1.00 C
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| 10 |
+
ATOM 25 O2 OCB X 2 24.274 22.507 21.064 1.00 1.00 O
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| 11 |
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ATOM 26 C9 OCB X 2 23.951 21.342 20.381 1.00 1.00 C
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ATOM 27 C10 OCB X 2 23.137 21.377 19.226 1.00 1.00 C
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ATOM 28 C11 OCB X 2 22.782 20.136 18.629 1.00 1.00 C
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ATOM 29 C12 OCB X 2 24.324 20.136 20.962 1.00 1.00 C
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ATOM 30 C13 OCB X 2 23.137 18.896 19.226 1.00 1.00 C
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ATOM 31 C14 OCB X 2 23.951 18.931 20.381 1.00 1.00 C
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ATOM 32 O3 OCB X 2 24.274 17.765 21.064 1.00 1.00 O
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ATOM 33 C15 OCB X 2 22.744 17.528 18.579 1.00 1.00 C
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ATOM 34 C16 OCB X 2 21.377 17.135 19.226 1.00 1.00 C
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ATOM 35 C17 OCB X 2 21.342 16.321 20.381 1.00 1.00 C
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ATOM 36 C18 OCB X 2 23.163 17.109 21.851 1.00 1.00 C
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ATOM 37 O4 OCB X 2 22.507 15.998 21.064 1.00 1.00 O
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| 23 |
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ATOM 38 O5 OCB X 2 17.765 24.274 21.064 1.00 1.00 O
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| 24 |
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ATOM 39 C19 OCB X 2 17.528 22.744 18.579 1.00 1.00 C
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| 25 |
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ATOM 40 C20 OCB X 2 17.135 21.377 19.226 1.00 1.00 C
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| 26 |
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ATOM 41 O6 OCB X 2 15.998 22.507 21.064 1.00 1.00 O
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| 27 |
+
ATOM 42 C21 OCB X 2 16.321 21.342 20.381 1.00 1.00 C
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| 28 |
+
ATOM 43 C22 OCB X 2 20.136 15.948 20.962 1.00 1.00 C
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| 29 |
+
ATOM 44 C23 OCB X 2 18.931 16.321 20.381 1.00 1.00 C
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| 30 |
+
ATOM 45 C24 OCB X 2 15.948 20.136 20.962 1.00 1.00 C
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| 31 |
+
ATOM 46 C25 OCB X 2 16.321 18.931 20.381 1.00 1.00 C
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| 32 |
+
ATOM 47 O7 OCB X 2 17.765 15.998 21.064 1.00 1.00 O
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| 33 |
+
ATOM 48 O8 OCB X 2 15.998 17.765 21.064 1.00 1.00 O
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| 34 |
+
ATOM 49 C26 OCB X 2 17.109 17.109 21.851 1.00 1.00 C
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| 35 |
+
ATOM 50 C27 OCB X 2 17.490 20.136 18.629 1.00 1.00 C
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| 36 |
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ATOM 51 C28 OCB X 2 17.135 18.896 19.226 1.00 1.00 C
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| 37 |
+
ATOM 52 C29 OCB X 2 20.136 17.490 18.629 1.00 1.00 C
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| 38 |
+
ATOM 53 C30 OCB X 2 17.528 17.528 18.579 1.00 1.00 C
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| 39 |
+
ATOM 54 C31 OCB X 2 18.896 17.135 19.226 1.00 1.00 C
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| 40 |
+
ATOM 55 C32 OCB X 2 17.109 23.163 21.851 1.00 1.00 C
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| 41 |
+
END
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calixarene/G1/data/md.tpr
ADDED
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version https://git-lfs.github.com/spec/v1
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oid sha256:5c89ae650b3f866ed703927ac8c05038cd8c752a04fa7a13ff22a5af2e67c241
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size 222776
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calixarene/G1/data/no_water.gro
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|
| 1 |
+
Generic title t= 22949.00000 step= 11474500
|
| 2 |
+
211
|
| 3 |
+
1MOL C1 1 1.347 0.428 2.338
|
| 4 |
+
1MOL C2 2 1.421 0.363 2.404
|
| 5 |
+
1MOL C3 3 1.515 0.298 2.496
|
| 6 |
+
1MOL C4 4 1.655 0.269 2.439
|
| 7 |
+
1MOL C5 5 1.770 0.225 2.531
|
| 8 |
+
1MOL C6 6 1.829 0.346 2.598
|
| 9 |
+
1MOL O1 7 1.812 0.372 2.716
|
| 10 |
+
1MOL O2 8 1.870 0.434 2.526
|
| 11 |
+
1MOL H1 9 1.275 0.490 2.290
|
| 12 |
+
1MOL H2 10 1.521 0.364 2.582
|
| 13 |
+
1MOL H3 11 1.467 0.204 2.524
|
| 14 |
+
1MOL H4 12 1.647 0.194 2.360
|
| 15 |
+
1MOL H5 13 1.681 0.358 2.381
|
| 16 |
+
1MOL H6 14 1.733 0.155 2.607
|
| 17 |
+
1MOL H7 15 1.840 0.167 2.471
|
| 18 |
+
2OCB C1 16 2.715 0.606 3.834
|
| 19 |
+
2OCB C2 17 2.452 0.679 3.886
|
| 20 |
+
2OCB C3 18 2.655 0.574 3.955
|
| 21 |
+
2OCB C4 19 2.644 0.679 3.740
|
| 22 |
+
2OCB C5 20 2.514 0.717 3.767
|
| 23 |
+
2OCB C6 21 2.528 0.622 3.986
|
| 24 |
+
2OCB O1 22 2.320 0.716 3.889
|
| 25 |
+
2OCB C7 23 2.460 0.588 0.085
|
| 26 |
+
2OCB C8 24 2.212 0.622 3.886
|
| 27 |
+
2OCB O2 25 2.188 0.588 4.024
|
| 28 |
+
2OCB C9 26 2.244 0.470 0.035
|
| 29 |
+
2OCB C10 27 2.377 0.462 0.075
|
| 30 |
+
2OCB C11 28 2.443 0.341 0.082
|
| 31 |
+
2OCB C12 29 2.168 0.354 0.036
|
| 32 |
+
2OCB C13 30 2.372 0.223 0.066
|
| 33 |
+
2OCB C14 31 2.235 0.233 0.045
|
| 34 |
+
2OCB O3 32 2.168 0.120 0.003
|
| 35 |
+
2OCB C15 33 2.439 0.088 0.083
|
| 36 |
+
2OCB C16 34 2.499 0.040 3.986
|
| 37 |
+
2OCB C17 35 2.419 4.019 3.886
|
| 38 |
+
2OCB C18 36 2.194 0.085 3.899
|
| 39 |
+
2OCB O4 37 2.283 4.004 3.901
|
| 40 |
+
2OCB O5 38 2.697 0.711 3.617
|
| 41 |
+
2OCB C19 39 2.857 0.560 3.808
|
| 42 |
+
2OCB C20 40 2.851 0.432 3.727
|
| 43 |
+
2OCB O6 41 2.830 0.554 3.519
|
| 44 |
+
2OCB C21 42 2.844 0.437 3.589
|
| 45 |
+
2OCB C22 43 2.477 3.979 3.766
|
| 46 |
+
2OCB C23 44 2.610 4.004 3.737
|
| 47 |
+
2OCB C24 45 2.846 0.317 3.518
|
| 48 |
+
2OCB C25 46 2.840 0.198 3.589
|
| 49 |
+
2OCB O7 47 2.655 3.976 3.610
|
| 50 |
+
2OCB O8 48 2.800 0.089 3.517
|
| 51 |
+
2OCB C26 49 2.659 0.056 3.521
|
| 52 |
+
2OCB C27 50 2.848 0.312 3.797
|
| 53 |
+
2OCB C28 51 2.843 0.192 3.728
|
| 54 |
+
2OCB C29 52 2.635 0.055 3.960
|
| 55 |
+
2OCB C30 53 2.834 0.060 3.802
|
| 56 |
+
2OCB C31 54 2.691 0.026 3.836
|
| 57 |
+
2OCB C32 55 2.698 0.610 3.514
|
| 58 |
+
2OCB C33 56 2.536 0.081 0.202
|
| 59 |
+
2OCB C34 57 2.561 3.970 0.250
|
| 60 |
+
2OCB C35 58 2.543 3.966 0.400
|
| 61 |
+
2OCB O9 59 2.433 3.982 0.451
|
| 62 |
+
2OCB C36 60 2.551 0.593 0.209
|
| 63 |
+
2OCB C37 61 2.623 0.728 0.209
|
| 64 |
+
2OCB C38 62 2.686 0.751 0.344
|
| 65 |
+
2OCB O10 63 2.686 0.862 0.393
|
| 66 |
+
2OCB C39 64 2.949 0.558 3.930
|
| 67 |
+
2OCB C40 65 3.088 0.499 3.904
|
| 68 |
+
2OCB C41 66 3.162 0.441 4.022
|
| 69 |
+
2OCB O11 67 3.199 0.513 0.080
|
| 70 |
+
2OCB C42 68 2.939 0.048 3.913
|
| 71 |
+
2OCB C43 69 2.925 3.947 3.987
|
| 72 |
+
2OCB C44 70 3.010 3.921 0.077
|
| 73 |
+
2OCB O12 71 2.970 3.856 0.171
|
| 74 |
+
2OCB C45 72 2.094 0.686 3.816
|
| 75 |
+
2OCB C46 73 1.885 0.763 3.645
|
| 76 |
+
2OCB C47 74 1.965 0.643 3.840
|
| 77 |
+
2OCB C48 75 2.115 0.767 3.705
|
| 78 |
+
2OCB C49 76 2.013 0.808 3.620
|
| 79 |
+
2OCB C50 77 1.863 0.676 3.751
|
| 80 |
+
2OCB C51 78 2.675 0.655 3.371
|
| 81 |
+
2OCB C52 79 2.580 0.709 3.117
|
| 82 |
+
2OCB C53 80 2.731 0.587 3.264
|
| 83 |
+
2OCB C54 81 2.575 0.749 3.354
|
| 84 |
+
2OCB C55 82 2.526 0.773 3.227
|
| 85 |
+
2OCB C56 83 2.684 0.620 3.137
|
| 86 |
+
2OCB C57 84 2.616 0.004 3.385
|
| 87 |
+
2OCB C58 85 2.507 3.973 3.137
|
| 88 |
+
2OCB C59 86 2.504 3.954 3.379
|
| 89 |
+
2OCB C60 87 2.676 0.044 3.267
|
| 90 |
+
2OCB C61 88 2.621 0.019 3.142
|
| 91 |
+
2OCB C62 89 2.451 3.925 3.255
|
| 92 |
+
2OCB C63 90 2.061 0.060 3.831
|
| 93 |
+
2OCB C64 91 1.839 0.042 3.671
|
| 94 |
+
2OCB C65 92 2.070 4.023 3.712
|
| 95 |
+
2OCB C66 93 1.941 0.114 3.875
|
| 96 |
+
2OCB C67 94 1.829 0.104 3.795
|
| 97 |
+
2OCB C68 95 1.957 4.013 3.632
|
| 98 |
+
2OCB O13 96 2.410 0.843 3.203
|
| 99 |
+
2OCB O14 97 2.667 0.083 3.030
|
| 100 |
+
2OCB O15 98 2.344 3.840 3.245
|
| 101 |
+
2OCB O16 99 2.039 0.891 3.513
|
| 102 |
+
2OCB O17 100 1.736 0.642 3.791
|
| 103 |
+
2OCB O18 101 1.967 3.960 3.506
|
| 104 |
+
2OCB O19 102 1.707 0.162 3.821
|
| 105 |
+
2OCB C69 103 2.748 0.194 3.033
|
| 106 |
+
2OCB C70 104 2.919 0.407 3.036
|
| 107 |
+
2OCB C71 105 2.693 0.321 3.036
|
| 108 |
+
2OCB C72 106 2.885 0.173 3.028
|
| 109 |
+
2OCB C73 107 2.974 0.280 3.032
|
| 110 |
+
2OCB C74 108 2.782 0.426 3.028
|
| 111 |
+
2OCB O20 109 2.744 0.558 3.030
|
| 112 |
+
2OCB C75 110 2.100 0.839 3.401
|
| 113 |
+
2OCB C76 111 2.230 0.699 3.196
|
| 114 |
+
2OCB C77 112 2.048 0.725 3.342
|
| 115 |
+
2OCB C78 113 2.224 0.882 3.356
|
| 116 |
+
2OCB C79 114 2.287 0.810 3.255
|
| 117 |
+
2OCB C80 115 2.106 0.653 3.238
|
| 118 |
+
2OCB C81 116 2.255 3.809 3.345
|
| 119 |
+
2OCB C82 117 2.077 3.752 3.546
|
| 120 |
+
2OCB C83 118 2.276 3.700 3.428
|
| 121 |
+
2OCB C84 119 2.142 3.888 3.359
|
| 122 |
+
2OCB C85 120 2.060 3.866 3.469
|
| 123 |
+
2OCB C86 121 2.181 3.663 3.522
|
| 124 |
+
2OCB C87 122 2.198 3.549 3.616
|
| 125 |
+
2OCB O21 123 2.295 3.477 3.607
|
| 126 |
+
2OCB C88 124 1.613 0.441 0.183
|
| 127 |
+
2OCB O22 125 1.614 0.550 0.236
|
| 128 |
+
2OCB C89 126 2.049 0.523 3.194
|
| 129 |
+
2OCB O23 127 2.049 0.488 3.077
|
| 130 |
+
2OCB O24 128 2.634 3.941 0.477
|
| 131 |
+
2OCB O25 129 3.114 3.982 0.088
|
| 132 |
+
2OCB O26 130 3.166 0.321 0.009
|
| 133 |
+
2OCB C90 131 3.121 0.260 3.024
|
| 134 |
+
2OCB O27 132 3.169 0.158 3.069
|
| 135 |
+
2OCB O28 133 1.566 0.351 0.250
|
| 136 |
+
2OCB O29 134 2.133 3.536 3.718
|
| 137 |
+
2OCB O30 135 3.191 0.352 2.988
|
| 138 |
+
2OCB O31 136 1.975 0.469 3.273
|
| 139 |
+
2OCB O32 137 2.747 0.665 0.404
|
| 140 |
+
2OCB C91 138 1.706 0.526 3.859
|
| 141 |
+
2OCB C92 139 1.651 0.300 4.008
|
| 142 |
+
2OCB C93 140 1.722 0.400 3.803
|
| 143 |
+
2OCB C94 141 1.667 0.535 3.992
|
| 144 |
+
2OCB C95 142 1.639 0.424 0.038
|
| 145 |
+
2OCB C96 143 1.694 0.287 3.877
|
| 146 |
+
2OCB C97 144 1.764 0.380 3.659
|
| 147 |
+
2OCB C98 145 2.283 1.006 3.420
|
| 148 |
+
2OCB C99 146 2.543 0.334 3.051
|
| 149 |
+
2OCB C 147 2.110 4.008 3.274
|
| 150 |
+
2OCB H1 148 2.706 0.516 4.031
|
| 151 |
+
2OCB H2 149 2.452 0.761 3.689
|
| 152 |
+
2OCB H3 150 2.389 0.667 0.108
|
| 153 |
+
2OCB H4 151 2.244 0.532 3.831
|
| 154 |
+
2OCB H5 152 2.549 0.331 0.105
|
| 155 |
+
2OCB H6 153 2.062 0.357 0.013
|
| 156 |
+
2OCB H7 154 2.356 0.023 0.112
|
| 157 |
+
2OCB H8 155 2.246 0.163 3.841
|
| 158 |
+
2OCB H9 156 2.898 0.642 3.748
|
| 159 |
+
2OCB H10 157 2.411 3.932 3.693
|
| 160 |
+
2OCB H11 158 2.851 0.315 3.410
|
| 161 |
+
2OCB H12 159 2.595 0.141 3.548
|
| 162 |
+
2OCB H13 160 2.853 0.310 3.906
|
| 163 |
+
2OCB H14 161 2.711 0.097 4.024
|
| 164 |
+
2OCB H15 162 2.868 4.022 3.726
|
| 165 |
+
2OCB H16 163 2.625 0.531 3.537
|
| 166 |
+
2OCB H17 164 2.631 0.133 0.194
|
| 167 |
+
2OCB H18 165 2.480 0.134 0.279
|
| 168 |
+
2OCB H19 166 2.484 3.903 0.210
|
| 169 |
+
2OCB H20 167 2.661 3.941 0.216
|
| 170 |
+
2OCB H21 168 2.629 0.517 0.214
|
| 171 |
+
2OCB H22 169 2.493 0.589 0.301
|
| 172 |
+
2OCB H23 170 2.699 0.740 0.132
|
| 173 |
+
2OCB H24 171 2.547 0.805 0.194
|
| 174 |
+
2OCB H25 172 2.955 0.658 3.975
|
| 175 |
+
2OCB H26 173 2.905 0.497 4.009
|
| 176 |
+
2OCB H27 174 3.072 0.412 3.839
|
| 177 |
+
2OCB H28 175 3.147 0.569 3.844
|
| 178 |
+
2OCB H29 176 3.038 0.052 3.867
|
| 179 |
+
2OCB H30 177 2.931 0.133 3.981
|
| 180 |
+
2OCB H31 178 2.820 3.938 4.017
|
| 181 |
+
2OCB H32 179 2.943 3.870 3.911
|
| 182 |
+
2OCB H33 180 1.798 0.796 3.588
|
| 183 |
+
2OCB H34 181 1.945 0.575 3.923
|
| 184 |
+
2OCB H35 182 2.216 0.797 3.681
|
| 185 |
+
2OCB H36 183 2.544 0.739 3.019
|
| 186 |
+
2OCB H37 184 2.804 0.508 3.278
|
| 187 |
+
2OCB H38 185 2.519 0.791 3.437
|
| 188 |
+
2OCB H39 186 2.458 3.957 3.041
|
| 189 |
+
2OCB H40 187 2.456 3.927 3.473
|
| 190 |
+
2OCB H41 188 2.764 0.108 3.271
|
| 191 |
+
2OCB H42 189 1.751 0.045 3.607
|
| 192 |
+
2OCB H43 190 2.159 3.965 3.685
|
| 193 |
+
2OCB H44 191 1.934 0.170 3.968
|
| 194 |
+
2OCB H45 192 2.980 0.497 3.033
|
| 195 |
+
2OCB H46 193 2.926 0.073 3.023
|
| 196 |
+
2OCB H47 194 2.285 0.659 3.111
|
| 197 |
+
2OCB H48 195 1.960 0.682 3.388
|
| 198 |
+
2OCB H49 196 2.013 3.735 3.632
|
| 199 |
+
2OCB H50 197 2.359 3.630 3.419
|
| 200 |
+
2OCB H51 198 1.626 0.209 0.030
|
| 201 |
+
2OCB H52 199 1.656 0.630 0.012
|
| 202 |
+
2OCB H53 200 1.871 0.362 3.653
|
| 203 |
+
2OCB H54 201 1.721 0.293 3.609
|
| 204 |
+
2OCB H55 202 1.745 0.462 3.589
|
| 205 |
+
2OCB H56 203 2.261 1.005 3.527
|
| 206 |
+
2OCB H57 204 2.391 1.011 3.409
|
| 207 |
+
2OCB H58 205 2.245 1.102 3.385
|
| 208 |
+
2OCB H59 206 2.484 0.268 2.987
|
| 209 |
+
2OCB H60 207 2.515 0.309 3.153
|
| 210 |
+
2OCB H61 208 2.515 0.438 3.031
|
| 211 |
+
2OCB H62 209 2.002 4.017 3.261
|
| 212 |
+
2OCB H63 210 2.148 0.068 3.319
|
| 213 |
+
2OCB H64 211 2.154 3.999 3.174
|
| 214 |
+
4.03244 4.03244 4.03244
|
calixarene/G1/data/plumed.dat
ADDED
|
@@ -0,0 +1,19 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
HOST: GROUP ATOMS=16-211 #host atoms
|
| 2 |
+
LIGC: GROUP ATOMS=1-6 #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
|
calixarene/G1/data/u.gro
ADDED
|
The diff for this file is too large to render.
See raw diff
|
|
|
calixarene/G1/traj/traj_com_0.trr
ADDED
|
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size 107026764
|
calixarene/G1/traj/traj_com_1.trr
ADDED
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version https://git-lfs.github.com/spec/v1
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size 94262688
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calixarene/G1/traj/traj_com_10.trr
ADDED
|
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version https://git-lfs.github.com/spec/v1
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size 53029392
|
calixarene/G1/traj/traj_com_11.trr
ADDED
|
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version https://git-lfs.github.com/spec/v1
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oid sha256:907bb965771a42fd1d65acd3d5cca6329326be95bf30ea0a7194481dd245cc8f
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size 59651436
|
calixarene/G1/traj/traj_com_12.trr
ADDED
|
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|
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| 1 |
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version https://git-lfs.github.com/spec/v1
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oid sha256:a91cfba434cb606fc31ad3c38832d0b73954378d83ccd250cd4934a79b4d588b
|
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size 59338500
|
calixarene/G1/traj/traj_com_13.trr
ADDED
|
@@ -0,0 +1,3 @@
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|
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|
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|
| 1 |
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version https://git-lfs.github.com/spec/v1
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oid sha256:26fd9fda49e1697e63657df6dc41df445f59a04d8f308df0635cde7194e46e3f
|
| 3 |
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size 101632596
|
calixarene/G1/traj/traj_com_14.trr
ADDED
|
@@ -0,0 +1,3 @@
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|
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|
|
|
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|
|
|
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|
| 1 |
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version https://git-lfs.github.com/spec/v1
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oid sha256:5a6a09a1a1214218a878c68f1edef9fd62f1995217aa693b1875309a2d01d001
|
| 3 |
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size 29604276
|
calixarene/G1/traj/traj_com_15.trr
ADDED
|
@@ -0,0 +1,3 @@
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|
| 1 |
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version https://git-lfs.github.com/spec/v1
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oid sha256:a040930d9010634b770573bfc620acc1e9fdfbcd8585735155c4f510225c15ae
|
| 3 |
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size 71566872
|
calixarene/G1/traj/traj_com_2.trr
ADDED
|
@@ -0,0 +1,3 @@
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| 1 |
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version https://git-lfs.github.com/spec/v1
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oid sha256:d4a6d3f058cb39505b288c97febd9f69e9ad99c20203033153215cea8573dc56
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| 3 |
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size 77873328
|
calixarene/G1/traj/traj_com_3.trr
ADDED
|
@@ -0,0 +1,3 @@
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| 1 |
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version https://git-lfs.github.com/spec/v1
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oid sha256:9008663bd34d00e9f9bbf34564dd2a054d5074e98ba2aecf346ad5fbb74407cd
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| 3 |
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size 48022416
|
calixarene/G1/traj/traj_com_4.trr
ADDED
|
@@ -0,0 +1,3 @@
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|
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| 1 |
+
version https://git-lfs.github.com/spec/v1
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oid sha256:0c12747218025f3c766911863f78fb95b13a6739f706702859df6cb87c791347
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| 3 |
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size 41198820
|
calixarene/G1/traj/traj_com_5.trr
ADDED
|
@@ -0,0 +1,3 @@
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|
| 1 |
+
version https://git-lfs.github.com/spec/v1
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oid sha256:998fea3f2c910bcf4ea7f063737d289b75eeae6896a5e4afc7d9066f316e1ecd
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| 3 |
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size 80032056
|
calixarene/G1/traj/traj_com_6.trr
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
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|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
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oid sha256:081385859651137e457bb7308e8f5906382186f84dbfc9fce7fc1211e97978d7
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| 3 |
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size 29811132
|
calixarene/G1/traj/traj_com_7.trr
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
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oid sha256:aea481b155bd61e3cafcfac84f2c61d8eab0fb918d93db0185a47efb11d12ebb
|
| 3 |
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size 65324064
|
calixarene/G1/traj/traj_com_8.trr
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
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| 2 |
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oid sha256:e2b334eefb9c04e559807df714d7bb13d7dd01365f021f6c35e1e199c2634018
|
| 3 |
+
size 16193112
|
calixarene/G1/traj/traj_com_9.trr
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
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oid sha256:84bfe3deccd60889be185d9ddd901cf07e755356d665705aabac59fd179fd089
|
| 3 |
+
size 54395172
|
calixarene/G2/data/NVT.mdp
ADDED
|
@@ -0,0 +1,70 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
define =
|
| 2 |
+
|
| 3 |
+
; Integrator stuff
|
| 4 |
+
integrator = md ; steep or md
|
| 5 |
+
dt = 0.002
|
| 6 |
+
nsteps = 250000000 ; -1 no maximum
|
| 7 |
+
init-step = 0 ;
|
| 8 |
+
continuation = no
|
| 9 |
+
|
| 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
|
| 15 |
+
|
| 16 |
+
|
| 17 |
+
; 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
|
| 27 |
+
rcoulomb = 1.0
|
| 28 |
+
pme-order = 4
|
| 29 |
+
fourierspacing = 0.1
|
| 30 |
+
ewald-rtol = 1.e-5 ; splitting between real and reciprocal
|
| 31 |
+
ewald-geometry = 3d ; 3d or 3dc
|
| 32 |
+
|
| 33 |
+
IMD-group = non-Water
|
| 34 |
+
|
| 35 |
+
; T and P
|
| 36 |
+
tcoupl = v-rescale ; none, nose-hoover, v-rescale
|
| 37 |
+
nsttcouple = 10 ; 10 if not used
|
| 38 |
+
tc-grps = OCB MOL Water_and_ions
|
| 39 |
+
tau-t = 0.1 0.1 0.1 ; ps
|
| 40 |
+
ref-t = 300 300 300 ; K
|
| 41 |
+
pcoupl = no ;
|
| 42 |
+
pcoupltype = isotropic ;
|
| 43 |
+
compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1
|
| 44 |
+
refcoord-scaling = com
|
| 45 |
+
tau-p = 5.0 ; ps
|
| 46 |
+
ref-p = 1.0 ; bar
|
| 47 |
+
|
| 48 |
+
; Constraints
|
| 49 |
+
constraints = all-bonds ; constraints distances
|
| 50 |
+
constraint-algorithm = LINCS ; or SHAKE
|
| 51 |
+
lincs_iter = 1
|
| 52 |
+
lincs_order = 4
|
| 53 |
+
|
| 54 |
+
;Generate velocities
|
| 55 |
+
gen_vel = yes ; assign velocities from Maxwell distribution
|
| 56 |
+
gen_temp = 300 ; temperature for Maxwell distribution
|
| 57 |
+
gen_seed = -1 ; generate a random seed
|
| 58 |
+
|
| 59 |
+
|
| 60 |
+
; OUTPUT
|
| 61 |
+
; Output control
|
| 62 |
+
nstenergy = 1000 ; save energies
|
| 63 |
+
nstlog = 1000 ; update log file every
|
| 64 |
+
nstxout = 500 ; save coordinates every 1.0 ps
|
| 65 |
+
; nstxout-compressed replaces nstxtcout
|
| 66 |
+
|
| 67 |
+
; COM removal . There are more options like removing from groups or the frequency
|
| 68 |
+
comm-mode = linear ; linear, angular (removes linear and angular motion) or none
|
| 69 |
+
nstcomm = 100 ; frequency of removal of com motion
|
| 70 |
+
nstcalcenergy = 500
|
calixarene/G2/data/com.ndx
ADDED
|
The diff for this file is too large to render.
See raw diff
|
|
|
calixarene/G2/data/conf_template.pdb
ADDED
|
@@ -0,0 +1,41 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
ATOM 16 C1 OCB B 2 18.896 23.137 19.226 1.00 1.00 C
|
| 2 |
+
ATOM 17 C2 OCB B 2 21.342 23.951 20.381 1.00 1.00 C
|
| 3 |
+
ATOM 18 C3 OCB X 2 20.136 22.782 18.629 1.00 1.00 C
|
| 4 |
+
ATOM 19 C4 OCB X 2 18.931 23.951 20.381 1.00 1.00 C
|
| 5 |
+
ATOM 20 C5 OCB X 2 20.136 24.324 20.962 1.00 1.00 C
|
| 6 |
+
ATOM 21 C6 OCB X 2 21.377 23.137 19.226 1.00 1.00 C
|
| 7 |
+
ATOM 22 O1 OCB X 2 22.507 24.274 21.064 1.00 1.00 O
|
| 8 |
+
ATOM 23 C7 OCB X 2 22.744 22.744 18.579 1.00 1.00 C
|
| 9 |
+
ATOM 24 C8 OCB X 2 23.163 23.163 21.851 1.00 1.00 C
|
| 10 |
+
ATOM 25 O2 OCB X 2 24.274 22.507 21.064 1.00 1.00 O
|
| 11 |
+
ATOM 26 C9 OCB X 2 23.951 21.342 20.381 1.00 1.00 C
|
| 12 |
+
ATOM 27 C10 OCB X 2 23.137 21.377 19.226 1.00 1.00 C
|
| 13 |
+
ATOM 28 C11 OCB X 2 22.782 20.136 18.629 1.00 1.00 C
|
| 14 |
+
ATOM 29 C12 OCB X 2 24.324 20.136 20.962 1.00 1.00 C
|
| 15 |
+
ATOM 30 C13 OCB X 2 23.137 18.896 19.226 1.00 1.00 C
|
| 16 |
+
ATOM 31 C14 OCB X 2 23.951 18.931 20.381 1.00 1.00 C
|
| 17 |
+
ATOM 32 O3 OCB X 2 24.274 17.765 21.064 1.00 1.00 O
|
| 18 |
+
ATOM 33 C15 OCB X 2 22.744 17.528 18.579 1.00 1.00 C
|
| 19 |
+
ATOM 34 C16 OCB X 2 21.377 17.135 19.226 1.00 1.00 C
|
| 20 |
+
ATOM 35 C17 OCB X 2 21.342 16.321 20.381 1.00 1.00 C
|
| 21 |
+
ATOM 36 C18 OCB X 2 23.163 17.109 21.851 1.00 1.00 C
|
| 22 |
+
ATOM 37 O4 OCB X 2 22.507 15.998 21.064 1.00 1.00 O
|
| 23 |
+
ATOM 38 O5 OCB X 2 17.765 24.274 21.064 1.00 1.00 O
|
| 24 |
+
ATOM 39 C19 OCB X 2 17.528 22.744 18.579 1.00 1.00 C
|
| 25 |
+
ATOM 40 C20 OCB X 2 17.135 21.377 19.226 1.00 1.00 C
|
| 26 |
+
ATOM 41 O6 OCB X 2 15.998 22.507 21.064 1.00 1.00 O
|
| 27 |
+
ATOM 42 C21 OCB X 2 16.321 21.342 20.381 1.00 1.00 C
|
| 28 |
+
ATOM 43 C22 OCB X 2 20.136 15.948 20.962 1.00 1.00 C
|
| 29 |
+
ATOM 44 C23 OCB X 2 18.931 16.321 20.381 1.00 1.00 C
|
| 30 |
+
ATOM 45 C24 OCB X 2 15.948 20.136 20.962 1.00 1.00 C
|
| 31 |
+
ATOM 46 C25 OCB X 2 16.321 18.931 20.381 1.00 1.00 C
|
| 32 |
+
ATOM 47 O7 OCB X 2 17.765 15.998 21.064 1.00 1.00 O
|
| 33 |
+
ATOM 48 O8 OCB X 2 15.998 17.765 21.064 1.00 1.00 O
|
| 34 |
+
ATOM 49 C26 OCB X 2 17.109 17.109 21.851 1.00 1.00 C
|
| 35 |
+
ATOM 50 C27 OCB X 2 17.490 20.136 18.629 1.00 1.00 C
|
| 36 |
+
ATOM 51 C28 OCB X 2 17.135 18.896 19.226 1.00 1.00 C
|
| 37 |
+
ATOM 52 C29 OCB X 2 20.136 17.490 18.629 1.00 1.00 C
|
| 38 |
+
ATOM 53 C30 OCB X 2 17.528 17.528 18.579 1.00 1.00 C
|
| 39 |
+
ATOM 54 C31 OCB X 2 18.896 17.135 19.226 1.00 1.00 C
|
| 40 |
+
ATOM 55 C32 OCB X 2 17.109 23.163 21.851 1.00 1.00 C
|
| 41 |
+
END
|
calixarene/G2/data/md.tpr
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:9b0d42f767a025f2fce44abf90079f7249e62cf051e93b0f5bab91e9c3f99737
|
| 3 |
+
size 223004
|
calixarene/G2/data/no_water.gro
ADDED
|
@@ -0,0 +1,214 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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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 |
+
Generic title t= 40.00000 step= 20000
|
| 2 |
+
211
|
| 3 |
+
1MOL C1 1 1.294 0.690 2.192
|
| 4 |
+
1MOL C2 2 1.427 0.703 2.154
|
| 5 |
+
1MOL C3 3 1.468 0.775 2.043
|
| 6 |
+
1MOL C4 4 1.367 0.814 1.957
|
| 7 |
+
1MOL C5 5 1.238 0.828 2.007
|
| 8 |
+
1MOL C6 6 1.198 0.761 2.121
|
| 9 |
+
1MOL C7 7 1.604 0.796 2.002
|
| 10 |
+
1MOL N1 8 1.714 0.815 1.976
|
| 11 |
+
1MOL C8 9 1.055 0.740 2.159
|
| 12 |
+
1MOL O1 10 1.025 0.721 2.275
|
| 13 |
+
1MOL O2 11 0.971 0.778 2.080
|
| 14 |
+
1MOL H1 12 1.266 0.620 2.270
|
| 15 |
+
1MOL H2 13 1.499 0.649 2.214
|
| 16 |
+
1MOL H3 14 1.388 0.862 1.862
|
| 17 |
+
1MOL H4 15 1.160 0.881 1.953
|
| 18 |
+
2OCB C1 16 1.905 2.627 2.125
|
| 19 |
+
2OCB C2 17 1.723 2.645 2.343
|
| 20 |
+
2OCB C3 18 1.934 2.696 2.242
|
| 21 |
+
2OCB C4 19 1.785 2.556 2.123
|
| 22 |
+
2OCB C5 20 1.698 2.569 2.230
|
| 23 |
+
2OCB C6 21 1.845 2.712 2.347
|
| 24 |
+
2OCB O1 22 1.650 2.629 2.458
|
| 25 |
+
2OCB C7 23 1.879 2.794 2.470
|
| 26 |
+
2OCB C8 24 1.700 2.538 2.558
|
| 27 |
+
2OCB O2 25 1.757 2.613 2.667
|
| 28 |
+
2OCB C9 26 1.893 2.629 2.662
|
| 29 |
+
2OCB C10 27 1.957 2.715 2.573
|
| 30 |
+
2OCB C11 28 2.094 2.702 2.558
|
| 31 |
+
2OCB C12 29 1.973 2.554 2.747
|
| 32 |
+
2OCB C13 30 2.174 2.613 2.628
|
| 33 |
+
2OCB C14 31 2.109 2.536 2.723
|
| 34 |
+
2OCB O3 32 2.175 2.438 2.792
|
| 35 |
+
2OCB C15 33 2.324 2.598 2.613
|
| 36 |
+
2OCB C16 34 2.362 2.489 2.515
|
| 37 |
+
2OCB C17 35 2.382 2.360 2.562
|
| 38 |
+
2OCB C18 36 2.199 2.319 2.714
|
| 39 |
+
2OCB O4 37 2.340 2.311 2.683
|
| 40 |
+
2OCB O5 38 1.751 2.472 2.020
|
| 41 |
+
2OCB C19 39 1.999 2.625 2.007
|
| 42 |
+
2OCB C20 40 2.100 2.513 2.023
|
| 43 |
+
2OCB O6 41 1.939 2.357 1.934
|
| 44 |
+
2OCB C21 42 2.060 2.384 1.992
|
| 45 |
+
2OCB C22 43 2.432 2.265 2.474
|
| 46 |
+
2OCB C23 44 2.464 2.291 2.342
|
| 47 |
+
2OCB C24 45 2.144 2.275 2.006
|
| 48 |
+
2OCB C25 46 2.274 2.295 2.050
|
| 49 |
+
2OCB O7 47 2.489 2.182 2.262
|
| 50 |
+
2OCB O8 48 2.356 2.187 2.065
|
| 51 |
+
2OCB C26 49 2.371 2.131 2.197
|
| 52 |
+
2OCB C27 50 2.229 2.529 2.071
|
| 53 |
+
2OCB C28 51 2.316 2.422 2.088
|
| 54 |
+
2OCB C29 52 2.391 2.516 2.382
|
| 55 |
+
2OCB C30 53 2.452 2.450 2.148
|
| 56 |
+
2OCB C31 54 2.441 2.420 2.296
|
| 57 |
+
2OCB C32 55 1.822 2.347 2.017
|
| 58 |
+
2OCB C33 56 2.401 2.729 2.589
|
| 59 |
+
2OCB C34 57 2.552 2.713 2.607
|
| 60 |
+
2OCB C35 58 2.618 2.848 2.595
|
| 61 |
+
2OCB O9 59 2.617 2.923 2.691
|
| 62 |
+
2OCB C36 60 1.940 2.930 2.433
|
| 63 |
+
2OCB C37 61 1.949 3.021 2.556
|
| 64 |
+
2OCB C38 62 2.002 3.156 2.513
|
| 65 |
+
2OCB O10 63 2.121 3.169 2.492
|
| 66 |
+
2OCB C39 64 2.057 2.761 1.964
|
| 67 |
+
2OCB C40 65 2.117 2.760 1.822
|
| 68 |
+
2OCB C41 66 2.029 2.716 1.708
|
| 69 |
+
2OCB O11 67 2.050 2.613 1.647
|
| 70 |
+
2OCB C42 68 2.528 2.578 2.110
|
| 71 |
+
2OCB C43 69 2.679 2.569 2.139
|
| 72 |
+
2OCB C44 70 2.762 2.652 2.045
|
| 73 |
+
2OCB O12 71 2.779 2.770 2.067
|
| 74 |
+
2OCB C45 72 1.593 2.443 2.609
|
| 75 |
+
2OCB C46 73 1.402 2.270 2.711
|
| 76 |
+
2OCB C47 74 1.586 2.417 2.745
|
| 77 |
+
2OCB C48 75 1.497 2.385 2.527
|
| 78 |
+
2OCB C49 76 1.399 2.299 2.576
|
| 79 |
+
2OCB C50 77 1.495 2.327 2.797
|
| 80 |
+
2OCB C51 78 1.734 2.232 1.973
|
| 81 |
+
2OCB C52 79 1.598 1.989 1.932
|
| 82 |
+
2OCB C53 80 1.796 2.121 1.917
|
| 83 |
+
2OCB C54 81 1.603 2.215 2.018
|
| 84 |
+
2OCB C55 82 1.537 2.094 2.000
|
| 85 |
+
2OCB C56 83 1.731 2.001 1.894
|
| 86 |
+
2OCB C57 84 2.366 1.980 2.186
|
| 87 |
+
2OCB C58 85 2.331 1.699 2.192
|
| 88 |
+
2OCB C59 86 2.407 1.909 2.297
|
| 89 |
+
2OCB C60 87 2.301 1.914 2.082
|
| 90 |
+
2OCB C61 88 2.279 1.777 2.090
|
| 91 |
+
2OCB C62 89 2.386 1.771 2.297
|
| 92 |
+
2OCB C63 90 2.143 2.197 2.784
|
| 93 |
+
2OCB C64 91 2.016 1.973 2.901
|
| 94 |
+
2OCB C65 92 2.155 2.070 2.729
|
| 95 |
+
2OCB C66 93 2.064 2.209 2.897
|
| 96 |
+
2OCB C67 94 1.996 2.101 2.950
|
| 97 |
+
2OCB C68 95 2.090 1.961 2.784
|
| 98 |
+
2OCB O13 96 1.411 2.082 2.053
|
| 99 |
+
2OCB O14 97 2.214 1.706 1.993
|
| 100 |
+
2OCB O15 98 2.435 1.693 2.399
|
| 101 |
+
2OCB O16 99 1.310 2.234 2.495
|
| 102 |
+
2OCB O17 100 1.487 2.290 2.929
|
| 103 |
+
2OCB O18 101 2.112 1.834 2.737
|
| 104 |
+
2OCB O19 102 1.915 2.114 3.061
|
| 105 |
+
2OCB C69 103 2.132 1.764 1.899
|
| 106 |
+
2OCB C70 104 1.983 1.912 1.718
|
| 107 |
+
2OCB C71 105 2.002 1.798 1.933
|
| 108 |
+
2OCB C72 106 2.184 1.802 1.777
|
| 109 |
+
2OCB C73 107 2.111 1.872 1.682
|
| 110 |
+
2OCB C74 108 1.928 1.866 1.837
|
| 111 |
+
2OCB O20 109 1.793 1.887 1.850
|
| 112 |
+
2OCB C75 110 1.292 2.246 2.359
|
| 113 |
+
2OCB C76 111 1.294 2.280 2.087
|
| 114 |
+
2OCB C77 112 1.233 2.356 2.299
|
| 115 |
+
2OCB C78 113 1.351 2.148 2.280
|
| 116 |
+
2OCB C79 114 1.351 2.166 2.142
|
| 117 |
+
2OCB C80 115 1.225 2.375 2.162
|
| 118 |
+
2OCB C81 116 2.392 1.731 2.524
|
| 119 |
+
2OCB C82 117 2.335 1.802 2.783
|
| 120 |
+
2OCB C83 118 2.491 1.753 2.618
|
| 121 |
+
2OCB C84 119 2.260 1.751 2.559
|
| 122 |
+
2OCB C85 120 2.233 1.789 2.690
|
| 123 |
+
2OCB C86 121 2.468 1.779 2.752
|
| 124 |
+
2OCB C87 122 2.582 1.805 2.845
|
| 125 |
+
2OCB O21 123 2.696 1.809 2.805
|
| 126 |
+
2OCB C88 124 1.751 2.517 3.272
|
| 127 |
+
2OCB O22 125 1.656 2.572 3.322
|
| 128 |
+
2OCB C89 126 1.163 2.496 2.102
|
| 129 |
+
2OCB O23 127 1.182 2.519 1.985
|
| 130 |
+
2OCB O24 128 2.701 2.875 2.511
|
| 131 |
+
2OCB O25 129 2.821 2.597 1.955
|
| 132 |
+
2OCB O26 130 1.951 2.798 1.662
|
| 133 |
+
2OCB C90 131 2.167 1.908 1.549
|
| 134 |
+
2OCB O27 132 2.094 1.952 1.462
|
| 135 |
+
2OCB O28 133 1.861 2.543 3.316
|
| 136 |
+
2OCB O29 134 2.566 1.825 2.963
|
| 137 |
+
2OCB O30 135 2.283 1.892 1.517
|
| 138 |
+
2OCB O31 136 1.095 2.572 2.168
|
| 139 |
+
2OCB O32 137 1.929 3.232 2.453
|
| 140 |
+
2OCB C91 138 1.596 2.299 3.011
|
| 141 |
+
2OCB C92 139 1.837 2.315 3.152
|
| 142 |
+
2OCB C93 140 1.694 2.201 3.001
|
| 143 |
+
2OCB C94 141 1.617 2.403 3.101
|
| 144 |
+
2OCB C95 142 1.736 2.408 3.171
|
| 145 |
+
2OCB C96 143 1.818 2.211 3.062
|
| 146 |
+
2OCB C97 144 1.673 2.084 2.908
|
| 147 |
+
2OCB C98 145 1.415 2.023 2.334
|
| 148 |
+
2OCB C99 146 1.951 1.769 2.072
|
| 149 |
+
2OCB C 147 2.147 1.736 2.459
|
| 150 |
+
2OCB H1 148 2.030 2.745 2.256
|
| 151 |
+
2OCB H2 149 1.610 2.505 2.234
|
| 152 |
+
2OCB H3 150 1.787 2.821 2.523
|
| 153 |
+
2OCB H4 151 1.778 2.470 2.521
|
| 154 |
+
2OCB H5 152 2.146 2.749 2.475
|
| 155 |
+
2OCB H6 153 1.931 2.481 2.816
|
| 156 |
+
2OCB H7 154 2.355 2.575 2.715
|
| 157 |
+
2OCB H8 155 2.148 2.337 2.618
|
| 158 |
+
2OCB H9 156 1.945 2.600 1.916
|
| 159 |
+
2OCB H10 157 2.439 2.163 2.510
|
| 160 |
+
2OCB H11 158 2.108 2.178 1.972
|
| 161 |
+
2OCB H12 159 2.278 2.159 2.249
|
| 162 |
+
2OCB H13 160 2.256 2.631 2.098
|
| 163 |
+
2OCB H14 161 2.381 2.619 2.347
|
| 164 |
+
2OCB H15 162 2.510 2.368 2.105
|
| 165 |
+
2OCB H16 163 1.845 2.329 2.123
|
| 166 |
+
2OCB H17 164 2.363 2.768 2.494
|
| 167 |
+
2OCB H18 165 2.365 2.811 2.651
|
| 168 |
+
2OCB H19 166 2.574 2.668 2.704
|
| 169 |
+
2OCB H20 167 2.586 2.654 2.521
|
| 170 |
+
2OCB H21 168 1.874 2.974 2.358
|
| 171 |
+
2OCB H22 169 2.039 2.919 2.390
|
| 172 |
+
2OCB H23 170 1.854 3.036 2.607
|
| 173 |
+
2OCB H24 171 2.024 2.987 2.628
|
| 174 |
+
2OCB H25 172 1.980 2.837 1.974
|
| 175 |
+
2OCB H26 173 2.143 2.795 2.022
|
| 176 |
+
2OCB H27 174 2.148 2.862 1.797
|
| 177 |
+
2OCB H28 175 2.204 2.694 1.816
|
| 178 |
+
2OCB H29 176 2.522 2.587 2.001
|
| 179 |
+
2OCB H30 177 2.485 2.664 2.161
|
| 180 |
+
2OCB H31 178 2.699 2.600 2.242
|
| 181 |
+
2OCB H32 179 2.715 2.468 2.118
|
| 182 |
+
2OCB H33 180 1.329 2.200 2.752
|
| 183 |
+
2OCB H34 181 1.671 2.453 2.803
|
| 184 |
+
2OCB H35 182 1.497 2.406 2.421
|
| 185 |
+
2OCB H36 183 1.534 1.903 1.917
|
| 186 |
+
2OCB H37 184 1.902 2.128 1.893
|
| 187 |
+
2OCB H38 185 1.541 2.297 2.052
|
| 188 |
+
2OCB H39 186 2.318 1.591 2.194
|
| 189 |
+
2OCB H40 187 2.459 1.963 2.375
|
| 190 |
+
2OCB H41 188 2.274 1.973 1.995
|
| 191 |
+
2OCB H42 189 1.969 1.888 2.950
|
| 192 |
+
2OCB H43 190 2.210 2.061 2.636
|
| 193 |
+
2OCB H44 191 2.058 2.304 2.950
|
| 194 |
+
2OCB H45 192 1.924 1.960 1.641
|
| 195 |
+
2OCB H46 193 2.287 1.781 1.751
|
| 196 |
+
2OCB H47 194 1.297 2.283 1.978
|
| 197 |
+
2OCB H48 195 1.191 2.430 2.366
|
| 198 |
+
2OCB H49 196 2.311 1.835 2.884
|
| 199 |
+
2OCB H50 197 2.595 1.738 2.590
|
| 200 |
+
2OCB H51 198 1.929 2.314 3.211
|
| 201 |
+
2OCB H52 199 1.539 2.478 3.112
|
| 202 |
+
2OCB H53 200 1.708 1.994 2.958
|
| 203 |
+
2OCB H54 201 1.565 2.068 2.894
|
| 204 |
+
2OCB H55 202 1.732 2.098 2.817
|
| 205 |
+
2OCB H56 203 1.354 1.933 2.346
|
| 206 |
+
2OCB H57 204 1.493 1.995 2.264
|
| 207 |
+
2OCB H58 205 1.454 2.043 2.434
|
| 208 |
+
2OCB H59 206 1.945 1.863 2.128
|
| 209 |
+
2OCB H60 207 1.849 1.732 2.080
|
| 210 |
+
2OCB H61 208 2.018 1.707 2.132
|
| 211 |
+
2OCB H62 209 2.053 1.719 2.512
|
| 212 |
+
2OCB H63 210 2.130 1.830 2.407
|
| 213 |
+
2OCB H64 211 2.162 1.659 2.383
|
| 214 |
+
4.02731 4.02731 4.02731
|
calixarene/G2/data/plumed.dat
ADDED
|
@@ -0,0 +1,19 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
HOST: GROUP ATOMS=16-211 #host atoms
|
| 2 |
+
LIGC: GROUP ATOMS=1-7,9 #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
|
calixarene/G2/data/topol.top
ADDED
|
The diff for this file is too large to render.
See raw diff
|
|
|
calixarene/G2/data/u.gro
ADDED
|
The diff for this file is too large to render.
See raw diff
|
|
|
calixarene/G2/traj/traj_com_0.trr
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
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| 2 |
+
oid sha256:9c40b17089b4de73eb8aa54a408f628ec04338f2d0148447a84b552d0127c51e
|
| 3 |
+
size 265202652
|
calixarene/G2/traj/traj_com_1.trr
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
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| 2 |
+
oid sha256:36476b5d65b2e88518e90ae8172c0e62bdbbcd347bf6239ad119c15fc6bc0fc1
|
| 3 |
+
size 162472128
|
calixarene/G2/traj/traj_com_2.trr
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
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| 2 |
+
oid sha256:245bffab4047c51b1ad855f4a9cbf1f732c855fe7ea1d1777c3a352c1f47ea77
|
| 3 |
+
size 62268960
|
calixarene/G2/traj/traj_com_3.trr
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:eb87d085ed9b9e4996134808f2c13993be0bfaf066156c87dcb41776d5dec726
|
| 3 |
+
size 319263672
|
calixarene/G2/traj/traj_com_4.trr
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:01839f9c6e499de8e4569c73770aceb8c4786b18fd9e7e014c703585cf104e95
|
| 3 |
+
size 57901116
|
calixarene/G2/traj/traj_com_5.trr
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:04ef55eeeb97b75401fcea40dedec45371083fef7f0ac01cc17570c73d7da9f6
|
| 3 |
+
size 109936008
|
calixarene/G2/traj/traj_com_6.trr
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:c6f4f7e29473207f0936daae7e581849efaf8ce6167e0443c54bf427f34e6d68
|
| 3 |
+
size 72919392
|
calixarene/G2/traj/traj_com_7.trr
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:fdd88193cc544d0ed7e09c520b753dd5fdea01e4071b0a6768bc490302af48ac
|
| 3 |
+
size 275367768
|
calixarene/G2/traj/traj_com_8.trr
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:714d1651f4951100d52efaede9ceea32f84c9f99a6aaf88c464624651e0fd136
|
| 3 |
+
size 122883072
|
calixarene/G2/traj/traj_com_9.trr
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:a62aa582579f0d891161343d29da118a1234b5a2b192a5a9ec76b802b9dbe4fb
|
| 3 |
+
size 265202652
|
calixarene/G3/data/NVT.mdp
ADDED
|
@@ -0,0 +1,70 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
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|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
define =
|
| 2 |
+
|
| 3 |
+
; Integrator stuff
|
| 4 |
+
integrator = md ; steep or md
|
| 5 |
+
dt = 0.002
|
| 6 |
+
nsteps = 250000000 ; -1 no maximum
|
| 7 |
+
init-step = 0 ;
|
| 8 |
+
continuation = no
|
| 9 |
+
|
| 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
|
| 15 |
+
|
| 16 |
+
|
| 17 |
+
; 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
|
| 27 |
+
rcoulomb = 1.0
|
| 28 |
+
pme-order = 4
|
| 29 |
+
fourierspacing = 0.1
|
| 30 |
+
ewald-rtol = 1.e-5 ; splitting between real and reciprocal
|
| 31 |
+
ewald-geometry = 3d ; 3d or 3dc
|
| 32 |
+
|
| 33 |
+
IMD-group = non-Water
|
| 34 |
+
|
| 35 |
+
; T and P
|
| 36 |
+
tcoupl = v-rescale ; none, nose-hoover, v-rescale
|
| 37 |
+
nsttcouple = 10 ; 10 if not used
|
| 38 |
+
tc-grps = OCB MOL Water_and_ions
|
| 39 |
+
tau-t = 0.1 0.1 0.1 ; ps
|
| 40 |
+
ref-t = 300 300 300 ; K
|
| 41 |
+
pcoupl = no ;
|
| 42 |
+
pcoupltype = isotropic ;
|
| 43 |
+
compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1
|
| 44 |
+
refcoord-scaling = com
|
| 45 |
+
tau-p = 5.0 ; ps
|
| 46 |
+
ref-p = 1.0 ; bar
|
| 47 |
+
|
| 48 |
+
; Constraints
|
| 49 |
+
constraints = all-bonds ; constraints distances
|
| 50 |
+
constraint-algorithm = LINCS ; or SHAKE
|
| 51 |
+
lincs_iter = 1
|
| 52 |
+
lincs_order = 4
|
| 53 |
+
|
| 54 |
+
;Generate velocities
|
| 55 |
+
gen_vel = yes ; assign velocities from Maxwell distribution
|
| 56 |
+
gen_temp = 300 ; temperature for Maxwell distribution
|
| 57 |
+
gen_seed = -1 ; generate a random seed
|
| 58 |
+
|
| 59 |
+
|
| 60 |
+
; OUTPUT
|
| 61 |
+
; Output control
|
| 62 |
+
nstenergy = 1000 ; save energies
|
| 63 |
+
nstlog = 1000 ; update log file every
|
| 64 |
+
nstxout = 500 ; save coordinates every 1.0 ps
|
| 65 |
+
; nstxout-compressed replaces nstxtcout
|
| 66 |
+
|
| 67 |
+
; COM removal . There are more options like removing from groups or the frequency
|
| 68 |
+
comm-mode = linear ; linear, angular (removes linear and angular motion) or none
|
| 69 |
+
nstcomm = 100 ; frequency of removal of com motion
|
| 70 |
+
nstcalcenergy = 500
|
calixarene/G3/data/b.gro
ADDED
|
The diff for this file is too large to render.
See raw diff
|
|
|
calixarene/G3/data/com.ndx
ADDED
|
The diff for this file is too large to render.
See raw diff
|
|
|
calixarene/G3/data/conf_template.pdb
ADDED
|
@@ -0,0 +1,41 @@
|
|
|
|
|
|
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|
|
|
|
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|
|
|
| 1 |
+
ATOM 33 C1 OCB B 2 18.896 23.137 19.226 1.00 1.00 C
|
| 2 |
+
ATOM 34 C2 OCB B 2 21.342 23.951 20.381 1.00 1.00 C
|
| 3 |
+
ATOM 35 C3 OCB X 2 20.136 22.782 18.629 1.00 1.00 C
|
| 4 |
+
ATOM 36 C4 OCB X 2 18.931 23.951 20.381 1.00 1.00 C
|
| 5 |
+
ATOM 37 C5 OCB X 2 20.136 24.324 20.962 1.00 1.00 C
|
| 6 |
+
ATOM 38 C6 OCB X 2 21.377 23.137 19.226 1.00 1.00 C
|
| 7 |
+
ATOM 39 O1 OCB X 2 22.507 24.274 21.064 1.00 1.00 O
|
| 8 |
+
ATOM 40 C7 OCB X 2 22.744 22.744 18.579 1.00 1.00 C
|
| 9 |
+
ATOM 41 C8 OCB X 2 23.163 23.163 21.851 1.00 1.00 C
|
| 10 |
+
ATOM 42 O2 OCB X 2 24.274 22.507 21.064 1.00 1.00 O
|
| 11 |
+
ATOM 43 C9 OCB X 2 23.951 21.342 20.381 1.00 1.00 C
|
| 12 |
+
ATOM 44 C10 OCB X 2 23.137 21.377 19.226 1.00 1.00 C
|
| 13 |
+
ATOM 45 C11 OCB X 2 22.782 20.136 18.629 1.00 1.00 C
|
| 14 |
+
ATOM 46 C12 OCB X 2 24.324 20.136 20.962 1.00 1.00 C
|
| 15 |
+
ATOM 47 C13 OCB X 2 23.137 18.896 19.226 1.00 1.00 C
|
| 16 |
+
ATOM 48 C14 OCB X 2 23.951 18.931 20.381 1.00 1.00 C
|
| 17 |
+
ATOM 49 O3 OCB X 2 24.274 17.765 21.064 1.00 1.00 O
|
| 18 |
+
ATOM 50 C15 OCB X 2 22.744 17.528 18.579 1.00 1.00 C
|
| 19 |
+
ATOM 51 C16 OCB X 2 21.377 17.135 19.226 1.00 1.00 C
|
| 20 |
+
ATOM 52 C17 OCB X 2 21.342 16.321 20.381 1.00 1.00 C
|
| 21 |
+
ATOM 53 C18 OCB X 2 23.163 17.109 21.851 1.00 1.00 C
|
| 22 |
+
ATOM 54 O4 OCB X 2 22.507 15.998 21.064 1.00 1.00 O
|
| 23 |
+
ATOM 55 O5 OCB X 2 17.765 24.274 21.064 1.00 1.00 O
|
| 24 |
+
ATOM 56 C19 OCB X 2 17.528 22.744 18.579 1.00 1.00 C
|
| 25 |
+
ATOM 57 C20 OCB X 2 17.135 21.377 19.226 1.00 1.00 C
|
| 26 |
+
ATOM 58 O6 OCB X 2 15.998 22.507 21.064 1.00 1.00 O
|
| 27 |
+
ATOM 59 C21 OCB X 2 16.321 21.342 20.381 1.00 1.00 C
|
| 28 |
+
ATOM 60 C22 OCB X 2 20.136 15.948 20.962 1.00 1.00 C
|
| 29 |
+
ATOM 61 C23 OCB X 2 18.931 16.321 20.381 1.00 1.00 C
|
| 30 |
+
ATOM 62 C24 OCB X 2 15.948 20.136 20.962 1.00 1.00 C
|
| 31 |
+
ATOM 63 C25 OCB X 2 16.321 18.931 20.381 1.00 1.00 C
|
| 32 |
+
ATOM 64 O7 OCB X 2 17.765 15.998 21.064 1.00 1.00 O
|
| 33 |
+
ATOM 65 O8 OCB X 2 15.998 17.765 21.064 1.00 1.00 O
|
| 34 |
+
ATOM 66 C26 OCB X 2 17.109 17.109 21.851 1.00 1.00 C
|
| 35 |
+
ATOM 67 C27 OCB X 2 17.490 20.136 18.629 1.00 1.00 C
|
| 36 |
+
ATOM 68 C28 OCB X 2 17.135 18.896 19.226 1.00 1.00 C
|
| 37 |
+
ATOM 69 C29 OCB X 2 20.136 17.490 18.629 1.00 1.00 C
|
| 38 |
+
ATOM 70 C30 OCB X 2 17.528 17.528 18.579 1.00 1.00 C
|
| 39 |
+
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
|
calixarene/G3/data/md.tpr
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:cda1e9466f9287fe08e2e1daf25f0a5126abde9ed94ddb8e0973dd8a86a794a0
|
| 3 |
+
size 227812
|
calixarene/G3/data/no_water.gro
ADDED
|
@@ -0,0 +1,231 @@
|
|
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|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
Generic title t= 12112.00000 step= 6056000
|
| 2 |
+
228
|
| 3 |
+
1MOL C1 1 1.315 3.873 2.237
|
| 4 |
+
1MOL C2 2 1.339 3.725 2.271
|
| 5 |
+
1MOL C3 3 1.309 3.624 2.160
|
| 6 |
+
1MOL C4 4 1.409 3.635 2.044
|
| 7 |
+
1MOL C5 5 1.379 3.534 1.932
|
| 8 |
+
1MOL C6 6 1.416 3.392 1.977
|
| 9 |
+
1MOL N1 7 1.399 3.285 1.873
|
| 10 |
+
1MOL C7 8 1.399 3.145 1.927
|
| 11 |
+
1MOL C8 9 1.503 3.303 1.767
|
| 12 |
+
1MOL C9 10 1.267 3.316 1.810
|
| 13 |
+
1MOL H1 11 1.252 3.871 2.148
|
| 14 |
+
1MOL H2 12 1.260 3.919 2.318
|
| 15 |
+
1MOL H3 13 1.273 3.709 2.357
|
| 16 |
+
1MOL H4 14 1.442 3.731 2.307
|
| 17 |
+
1MOL H5 15 1.206 3.635 2.127
|
| 18 |
+
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
|
| 25 |
+
1MOL H13 23 1.408 3.925 2.210
|
| 26 |
+
1MOL H14 24 1.304 3.125 1.976
|
| 27 |
+
1MOL H15 25 1.413 3.080 1.840
|
| 28 |
+
1MOL H16 26 1.483 3.126 1.994
|
| 29 |
+
1MOL H17 27 1.490 3.219 1.698
|
| 30 |
+
1MOL H18 28 1.471 3.392 1.712
|
| 31 |
+
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
|
| 35 |
+
2OCB C1 33 2.395 0.048 3.524
|
| 36 |
+
2OCB C2 34 2.540 4.024 3.295
|
| 37 |
+
2OCB C3 35 2.491 0.136 3.477
|
| 38 |
+
2OCB C4 36 2.365 3.970 3.444
|
| 39 |
+
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
|
| 43 |
+
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
|
| 46 |
+
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
|
| 49 |
+
2OCB C13 47 2.497 0.521 3.189
|
| 50 |
+
2OCB C14 48 2.491 0.486 3.055
|
| 51 |
+
2OCB O3 49 2.416 0.568 2.974
|
| 52 |
+
2OCB C15 50 2.435 0.648 3.244
|
| 53 |
+
2OCB C16 51 2.294 0.621 3.291
|
| 54 |
+
2OCB C17 52 2.193 0.638 3.197
|
| 55 |
+
2OCB C18 53 2.273 0.554 2.983
|
| 56 |
+
2OCB O4 54 2.225 0.662 3.065
|
| 57 |
+
2OCB O5 55 2.256 3.895 3.479
|
| 58 |
+
2OCB C19 56 2.319 0.082 3.651
|
| 59 |
+
2OCB C20 57 2.198 0.167 3.623
|
| 60 |
+
2OCB O6 58 2.077 4.001 3.578
|
| 61 |
+
2OCB C21 59 2.076 0.103 3.603
|
| 62 |
+
2OCB C22 60 2.061 0.619 3.233
|
| 63 |
+
2OCB C23 61 2.028 0.588 3.364
|
| 64 |
+
2OCB C24 62 1.962 0.177 3.575
|
| 65 |
+
2OCB C25 63 1.971 0.315 3.577
|
| 66 |
+
2OCB O7 64 1.896 0.558 3.391
|
| 67 |
+
2OCB O8 65 1.859 0.382 3.535
|
| 68 |
+
2OCB C26 66 1.860 0.419 3.396
|
| 69 |
+
2OCB C27 67 2.200 0.304 3.641
|
| 70 |
+
2OCB C28 68 2.087 0.381 3.616
|
| 71 |
+
2OCB C29 69 2.257 0.580 3.418
|
| 72 |
+
2OCB C30 70 2.094 0.532 3.604
|
| 73 |
+
2OCB C31 71 2.125 0.566 3.460
|
| 74 |
+
2OCB C32 72 2.131 3.960 3.451
|
| 75 |
+
2OCB C33 73 2.536 0.709 3.342
|
| 76 |
+
2OCB C34 74 2.509 0.857 3.372
|
| 77 |
+
2OCB C35 75 2.604 0.935 3.459
|
| 78 |
+
2OCB O9 76 2.570 0.960 3.573
|
| 79 |
+
2OCB C36 77 2.757 0.277 3.422
|
| 80 |
+
2OCB C37 78 2.865 0.182 3.473
|
| 81 |
+
2OCB C38 79 2.916 0.239 3.603
|
| 82 |
+
2OCB O10 80 3.033 0.219 3.627
|
| 83 |
+
2OCB C39 81 2.413 0.128 3.763
|
| 84 |
+
2OCB C40 82 2.352 0.141 3.903
|
| 85 |
+
2OCB C41 83 2.465 0.170 3.999
|
| 86 |
+
2OCB O11 84 2.471 0.088 0.055
|
| 87 |
+
2OCB C42 85 2.175 0.603 3.713
|
| 88 |
+
2OCB C43 86 2.124 0.599 3.857
|
| 89 |
+
2OCB C44 87 1.994 0.674 3.864
|
| 90 |
+
2OCB O12 88 1.892 0.613 3.891
|
| 91 |
+
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
|
| 97 |
+
2OCB C51 95 2.026 3.870 3.389
|
| 98 |
+
2OCB C52 96 1.859 3.683 3.272
|
| 99 |
+
2OCB C53 97 1.891 3.869 3.422
|
| 100 |
+
2OCB C54 98 2.072 3.792 3.284
|
| 101 |
+
2OCB C55 99 1.989 3.697 3.226
|
| 102 |
+
2OCB C56 100 1.811 3.768 3.370
|
| 103 |
+
2OCB C57 101 1.731 0.387 3.325
|
| 104 |
+
2OCB C58 102 1.522 0.302 3.173
|
| 105 |
+
2OCB C59 103 1.712 0.444 3.200
|
| 106 |
+
2OCB C60 104 1.649 0.286 3.374
|
| 107 |
+
2OCB C61 105 1.543 0.242 3.296
|
| 108 |
+
2OCB C62 106 1.607 0.398 3.121
|
| 109 |
+
2OCB C63 107 2.212 0.547 2.846
|
| 110 |
+
2OCB C64 108 2.072 0.526 2.599
|
| 111 |
+
2OCB C65 109 2.083 0.597 2.828
|
| 112 |
+
2OCB C66 110 2.268 0.483 2.736
|
| 113 |
+
2OCB C67 111 2.196 0.465 2.619
|
| 114 |
+
2OCB C68 112 2.017 0.593 2.707
|
| 115 |
+
2OCB O13 113 2.034 3.606 3.134
|
| 116 |
+
2OCB O14 114 1.456 0.142 3.331
|
| 117 |
+
2OCB O15 115 1.572 0.451 2.999
|
| 118 |
+
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
|
| 121 |
+
2OCB O19 119 2.245 0.392 2.513
|
| 122 |
+
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
|
| 127 |
+
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
|
| 131 |
+
2OCB C77 129 2.432 3.538 3.065
|
| 132 |
+
2OCB C78 130 2.226 3.634 2.993
|
| 133 |
+
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
|
| 137 |
+
2OCB C83 135 1.573 0.684 2.955
|
| 138 |
+
2OCB C84 136 1.743 0.542 2.860
|
| 139 |
+
2OCB C85 137 1.790 0.652 2.790
|
| 140 |
+
2OCB C86 138 1.616 0.791 2.877
|
| 141 |
+
2OCB C87 139 1.530 0.912 2.881
|
| 142 |
+
2OCB O21 140 1.564 1.015 2.828
|
| 143 |
+
2OCB C88 141 2.723 0.378 2.398
|
| 144 |
+
2OCB O22 142 2.825 0.312 2.399
|
| 145 |
+
2OCB C89 143 2.450 3.411 3.283
|
| 146 |
+
2OCB O23 144 2.392 3.335 3.359
|
| 147 |
+
2OCB O24 145 2.711 0.971 3.414
|
| 148 |
+
2OCB O25 146 1.988 0.792 3.836
|
| 149 |
+
2OCB O26 147 2.523 0.277 3.996
|
| 150 |
+
2OCB C90 148 1.479 3.976 3.778
|
| 151 |
+
2OCB O27 149 1.444 0.042 3.840
|
| 152 |
+
2OCB O28 150 2.721 0.495 2.365
|
| 153 |
+
2OCB O29 151 1.433 0.917 2.955
|
| 154 |
+
2OCB O30 152 1.492 3.875 3.844
|
| 155 |
+
2OCB O31 153 2.571 3.415 3.286
|
| 156 |
+
2OCB O32 154 2.846 0.296 3.685
|
| 157 |
+
2OCB C91 155 2.490 0.120 2.540
|
| 158 |
+
2OCB C92 156 2.480 0.383 2.470
|
| 159 |
+
2OCB C93 157 2.371 0.190 2.552
|
| 160 |
+
2OCB C94 158 2.606 0.189 2.509
|
| 161 |
+
2OCB C95 159 2.604 0.321 2.467
|
| 162 |
+
2OCB C96 160 2.363 0.323 2.515
|
| 163 |
+
2OCB C97 161 2.243 0.119 2.592
|
| 164 |
+
2OCB C98 162 2.142 3.728 2.909
|
| 165 |
+
2OCB C99 163 1.586 3.948 3.211
|
| 166 |
+
2OCB C 164 1.798 0.401 2.851
|
| 167 |
+
2OCB H1 165 2.506 0.230 3.527
|
| 168 |
+
2OCB H2 166 2.404 3.857 3.265
|
| 169 |
+
2OCB H3 167 2.738 0.146 3.256
|
| 170 |
+
2OCB H4 168 2.460 0.082 3.088
|
| 171 |
+
2OCB H5 169 2.553 0.438 3.382
|
| 172 |
+
2OCB H6 170 2.537 0.345 2.893
|
| 173 |
+
2OCB H7 171 2.430 0.715 3.158
|
| 174 |
+
2OCB H8 172 2.239 0.462 3.033
|
| 175 |
+
2OCB H9 173 2.289 4.016 3.689
|
| 176 |
+
2OCB H10 174 1.979 0.635 3.163
|
| 177 |
+
2OCB H11 175 1.871 0.123 3.550
|
| 178 |
+
2OCB H12 176 1.942 0.358 3.356
|
| 179 |
+
2OCB H13 177 2.293 0.358 3.655
|
| 180 |
+
2OCB H14 178 2.334 0.560 3.492
|
| 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 |
+
2OCB H19 183 2.504 0.912 3.278
|
| 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
|
| 191 |
+
2OCB H25 189 2.493 0.052 3.761
|
| 192 |
+
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
|
| 204 |
+
2OCB H38 202 2.177 3.789 3.255
|
| 205 |
+
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
|
| 208 |
+
2OCB H42 206 2.024 0.523 2.502
|
| 209 |
+
2OCB H43 207 2.033 0.629 2.919
|
| 210 |
+
2OCB H44 208 2.364 0.436 2.750
|
| 211 |
+
2OCB H45 209 1.621 3.798 3.651
|
| 212 |
+
2OCB H46 210 1.415 0.136 3.582
|
| 213 |
+
2OCB H47 211 2.197 3.495 3.302
|
| 214 |
+
2OCB H48 212 2.535 3.515 3.041
|
| 215 |
+
2OCB H49 213 1.749 0.852 2.720
|
| 216 |
+
2OCB H50 214 1.490 0.690 3.026
|
| 217 |
+
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
|
| 220 |
+
2OCB H54 218 2.252 0.010 2.590
|
| 221 |
+
2OCB H55 219 2.210 0.141 2.694
|
| 222 |
+
2OCB H56 220 2.153 3.822 2.964
|
| 223 |
+
2OCB H57 221 2.175 3.745 2.806
|
| 224 |
+
2OCB H58 222 2.035 3.705 2.899
|
| 225 |
+
2OCB H59 223 1.517 4.009 3.152
|
| 226 |
+
2OCB H60 224 1.687 3.986 3.192
|
| 227 |
+
2OCB H61 225 1.572 3.844 3.182
|
| 228 |
+
2OCB H62 226 1.860 0.402 2.761
|
| 229 |
+
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
|
calixarene/G3/data/plumed.dat
ADDED
|
@@ -0,0 +1,19 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 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
|
calixarene/G3/data/run.sh
ADDED
|
@@ -0,0 +1,16 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
#!/bin/bash
|
| 2 |
+
#SBATCH -J G3
|
| 3 |
+
#SBATCH -o G3.log
|
| 4 |
+
#SBATCH -e G3.err
|
| 5 |
+
#SBATCH -N 1
|
| 6 |
+
#SBATCH -p gpu
|
| 7 |
+
#SBATCH --gres=gpu:1
|
| 8 |
+
#SBATCH --cpus-per-task=1
|
| 9 |
+
#SBATCH --ntasks=4
|
| 10 |
+
##SBATCH -w gpu05
|
| 11 |
+
|
| 12 |
+
module load cuda/11.8
|
| 13 |
+
newdir=./
|
| 14 |
+
nsteps=500000000 # 1us
|
| 15 |
+
gmx_mpi mdrun -plumed plumed.dat -nsteps $nsteps -s md.tpr
|
| 16 |
+
|