[gmx-users] Weird problem

[lina]

There might be relevant to walltime settings. There might be a default limit.

try qsub -l walltime=1000:00:00 yourjob

adjust the time or google further to meet your need.


On Fri, Jul 15, 2011 at 2:27 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> Sayan Bagchi wrote:
>>
>> Hello All,
>> I am having a weird problem and I do not know whether it has to do
>> anything with Gromacs or the cluster setting I am using.
>> When I run a MD simulation (on any protein), the job automatically
>> terminates overnight without an error message. I mean if I start the job
>> early in the morning it runs longer than if I start the job later in the
>> day. But it never runs to the desired length mentioned in the .mdp file.
>>
>
> If you are not receiving any error messages from Gromacs, then it is
> something your system is doing that is unrelated to mdrun.  Contact your
> system administrators.  Some queues employ systems to purge jobs after a
> certain amount of time or even stop all jobs at a certain time of day to
> allow other jobs to start.
>
> -Justin
>
>> I am copying the .mdp file:
>>
>> -----------------------------------------------------
>>
>> integrator      = md
>> nsteps          = 5000000
>> dt              = 0.002
>> nstlist         = 10
>> nstcomm         = 1
>> rlist           = 1.0
>> coulombtype     = pme
>> rcoulomb        = 1.0
>> vdw-type        = cut-off
>> rvdw            = 1.0
>> tcoupl          = Nose-Hoover
>> tc-grps         = protein non-protein
>> tau-t           = 0.5 0.5
>> ref-t           = 298 298
>> Pcoupl              =  Parrinello-Rahman
>> pcoupltype          =  isotropic
>> tau_p               =  1.0
>> compressibility     =  4.5e-5
>> ref_p               =  1.0
>> nstxout         = 100
>> nstvout         = 100
>> nstxtcout       = 100
>> nstenergy       = 100
>> userint1        = 123
>> userint2        = 124
>> userint3        = 247
>> -----------------------------------------------------------
>>
>> Any thoughts?
>>
>> Sayan.
>>
>>
>>
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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-- 
Best Regards,

lina