Hi, I am trying to simulate a case where I am pulling a set of atoms with constant velocity with respect to another set of atoms, like:
XXXXXXXXXXXXXXXXXXXXXXXXXXX --> U (velocity, moving wall, pull group) ooooooooooooooooooooooooooo ooooooooooooooooooooooooooo -> fluid ooooooooooooooooooooooooooo XXXXXXXXXXXXXXXXXXXXXXXXXXX --> fixed wall (reference group) but while running mdrun for the case, it simply becomes unresponsive after 300 steps (no output message even with the -v option). Can somebody suggest what I might be missing. I am appending the md.log and .mdp file for reference however, for quick reference the excerpts are-> *) eql.mdp: ; COM PULLING ; Pull type: no, umbrella, constraint or constant_force pull = constraint pull_geometry = direction pull_start = yes pull_init = pull_nstxout = 10 pull_ngroups = 1 pull_group0 = WD pull_group1 = WU pull_vec1 = 1 0 0 pull_rate1 = 1 *) md.log: pull = constraint pull_geometry = direction pull_dim (3): pull_dim[0]=1 pull_dim[1]=1 pull_dim[2]=1 pull_r1 = 1 pull_r0 = 1.5 pull_constr_tol = 1e-06 pull_nstxout = 10 pull_nstfout = 1 pull_ngrp = 1 pull_group 0: atom (672): atom[0,...,671] = {672,...,1343} weight: not available pbcatom = 1007 vec (3): vec[0]= 0.00000e+00 vec[1]= 0.00000e+00 vec[2]= 0.00000e+00 init (3): init[0]= 0.00000e+00 init[1]= 0.00000e+00 init[2]= 0.00000e+00 rate = 0 k = 0 kB = 0 pull_group 1: atom (672): atom[0,...,671] = {0,...,671} weight: not available pbcatom = 335 vec (3): vec[0]= 1.00000e+00 vec[1]= 0.00000e+00 vec[2]= 0.00000e+00 init (3): init[0]= 2.08088e+00 init[1]= 0.00000e+00 init[2]= 0.00000e+00 rate = 1 k = 0 kB = 0 The other useful data might be: OS- Ubuntu 8.04 Gromacs- 4.0.2 Thanks, Manik Mayur -- Graduate student Microfluidics Lab Dept. of Mechanical Engg. IIT Kharagpur
md.log
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eql.mdp
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