[gmx-users] mdrun cpt

Mon Oct 28 20:16:01 CET 2013

No this isn't a problem. You can use job names under the -hold_jid flag.
As long as you change the job name in the submit script between
submissions this isn't a problem. You could have a submit script for job 4
with -N md_job4 and -hold_jid md_job3 then change these to -N md_job5 and
-hold_jid md_job4 for the next job. Then you can submit job 5 as soon as
you have made this change which will be within seconds of submitting job
4.

> Mark,
>
> The problem with one .tpr file set for 100ns is that when job number (say)
> 4 hits the wall limit, it crashes and never gets a chance to submit the
> next job. So it's not really automated.
>
> Now I could initiate job 5 before /mdrun/ in job 4's script and hold job 5
> till job 4 ends. But the PBS queuing system is sometime weird and takes a
> bit of time to recognize a job and give back its jobID. So I could submit
> job 5 but be unable to change its status to /hold/ because PBS does not
> return its ID. Another problem is that if resources are available, job 5
> could start before I ever get a chance to /hold/ it.
>
>
>
>
> On Mon, Oct 28, 2013 at 11:47 AM, Mark Abraham
> <mark.j.abraham at gmail.com>wrote:
>
>> On Mon, Oct 28, 2013 at 4:27 PM, Pavan Ghatty <pavan.gromacs at gmail.com
>> >wrote:
>>
>> > I have need to collect 100ns but I can collect only ~1ns (1000steps)
>> per
>> > run. Since I dont have .trr files, I rely on .cpt files for restarts.
>> For
>> > example,
>> >
>> > grompp -f md.mdp  -c md_14.gro -t md_14.cpt -p system.top -o md_15
>> >
>> > This runs into a problem when the run gets killed due to walltime
>> limits. I
>> > now have a .xtc file which has run (say) 700 steps and a .cpt file
>> which
>> > was last written at 600th step.
>> >
>>
>> You seem to have no need to use grompp, because you don't need to use a
>> workflow that generates multiple .tpr files. Do the equivalent of what
>> the
>> restart page advises: mdrun -s topol.tpr -cpi state.cpt. Thus, make a
>> .tpr
>> for the whole 100ns run, and then keep doing
>>
>> mdrun -s whole-run -cpi whateverwaslast -deffnm whateversuitsyouthistime
>>
>> with or without -append, perhaps with -maxh, keeping whatever manual
>> backups you feel necessary. Then perhaps concatenate your final
>> trajectory
>> files, according to your earlier choices.
>>
>> - To set up the next run I use the .cpt file from 600th step.
>> > - Now during analysis if I want to center the protein and such,
>> /trjconv/
>> > needs an .xtc and .tpr file but not a .cpt file. So how does /trjconv/
>> know
>> > to stop at 600th step?
>>
>>
>> trjconv just operates on the contents of the trajectory file, as
>> modified
>> by things like -b -e and -dt. The .tpr just gives it context, such as
>> atom
>> names. You could give it a .tpr from any point during the run.
>>
>> Mark
>>
>> If this has to be put in manually, it becomes
>> > cumbersome.
>> >
>> > Thoughts?
>> >
>> >
>> >
>> >
>> >
>> > On Sun, Oct 27, 2013 at 11:38 AM, Justin Lemkul <jalemkul at vt.edu>
>> wrote:
>> >
>> > >
>> > >
>> > > On 10/27/13 9:37 AM, Pavan Ghatty wrote:
>> > >
>> > >> Hello All,
>> > >>
>> > >> Is there a way to make mdrun put out .cpt file with the same
>> frequency
>> > as
>> > >> a
>> > >> .xtc or .trr file. From here
>> > >> http://www.gromacs.org/**Documentation/How-tos/Doing_**Restarts<
>> > http://www.gromacs.org/Documentation/How-tos/Doing_Restarts>I see that
>> we
>> > >> can choose how often (time in mins) the .cpt file is written. But
>> > clearly
>> > >> if the frequency of output of .cpt (frequency in mins) and .xtc
>> > (frequency
>> > >> in simulation steps) do not match, it can create problems during
>> > analysis;
>> > >> especially in the event of frequent crashes. Also, I am not storing
>> .trr
>> > >> file since I dont need that precision.
>> > >> I am using Gromacs 4.6.1.
>> > >>
>> > >>
>> > > What problems are you experiencing?  There is no need for .cpt
>> frequency
>> > > to be the same as .xtc frequency, because any duplicate frames
>> should
>> be
>> > > handled elegantly when appending.
>> > >
>> > > -Justin
>> > >
>> > > --
>> > > ==============================**====================
>> > >
>> > > Justin A. Lemkul, Ph.D.
>> > > Postdoctoral Fellow
>> > >
>> > > Department of Pharmaceutical Sciences
>> > > School of Pharmacy
>> > > Health Sciences Facility II, Room 601
>> > > University of Maryland, Baltimore
>> > > 20 Penn St.
>> > > Baltimore, MD 21201
>> > >
>> > > jalemkul at outerbanks.umaryland.**edu
>> <jalemkul at outerbanks.umaryland.edu
>> >
>> > | (410)
>> > > 706-7441
>> > >
>> > > ==============================**====================
>> > > --
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