[gmx-users] mdrun hangs with the pull option

[Manik Mayur]

On Tue, Mar 17, 2009 at 9:31 PM, Manik Mayur <manik.mayur at gmail.com> wrote:

>
>
> 2009/3/17 Berk Hess <gmx3 at hotmail.com>
>
>>  Hi,
>>
>> You pull rate is ridiculously high (1 nm/ps).
>>
>
Also I am simulating in reduced dimentions. I think it is fine then.

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
>



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