[gmx-users] mdrun cpt

[Pavan Ghatty]

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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