[gmx-users] mdrun cpt

[Pavan Ghatty]

Aah yes of course. Thanks James.



On Mon, Oct 28, 2013 at 3:16 PM, <jkrieger at mrc-lmb.cam.ac.uk> wrote:

> 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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