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
Description: Binary data
eql.mdp
Description: Binary data
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