[gmx-users] mdrun hangs with the pull option

[Manik Mayur]

2009/3/17 Berk Hess <gmx3 at hotmail.com>

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

Is there any upper limit on the pull rate?
btw are the other parameters consistent with the system I am trying to
simulate?


> 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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-- 
Graduate student
Microfluidics Lab
Dept. of Mechanical Engg.
IIT Kharagpur
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