[gmx-users] mdrun cpt

[Mark Abraham]

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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