[gmx-users] mdrun hangs with the pull option

[Berk Hess]

Hi,

You pull rate is ridiculously high (1 nm/ps).

Berk
 

Date: Tue, 17 Mar 2009 19:54:50 +0530
From: manik.mayur at gmail.com
To: gmx-users at gromacs.org
Subject: [gmx-users] mdrun hangs with the pull option

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

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