[gmx-users] Weird problem

[Justin A. Lemkul]

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.
> 
> 
> 

-- 
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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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