[gmx-users] Can't locate state.cpt for gmx mdrun

[Mark Abraham]

Hi,

Checkpoints continue unfinished calculations. Energy minimization generally
is short, and only stops when complete, so there is no meaningful restart.

Mark

On Mon, 10 Jul 2017 00:13 Yonatan Zelnik <yonatanzelnik at gmail.com> wrote:

> Hello Justin,
>
> I see now why there aren't checkpoint files being produced. I guess I
> wanted to checkpoint files, in case the EM didn't converge in n steps, then
> I could keep going from that point instead of starting over with >n steps.
>
> Thanks for the response.
>
> Yonatan
>
> On Fri, Jul 7, 2017 at 8:14 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
> >
> >
> > On 7/7/17 8:00 PM, Yonatan Zelnik wrote:
> >
> >> Hello,
> >>
> >> I am running an energy minimization script that works quite well, except
> >> that I can't find any of the checkpoint files that mdrun is supposed to
> >> provide. I've been looking through the docs for a while, and I can't
> seem
> >> to find a reason. I have tried the script on multiple systems, and
> >> multiple
> >> installations of gromacs (I am using 5.1.4 with MPI).
> >>
> >> Here is the mdrun command I am using:
> >>
> >> mdrun_sp -v -s em.tpr -o mintraj -g mdlog -c solvated.gro -x
> solvated_traj
> >> -cpo state.cpt -cpt 1.
> >>
> >> The -cpt 1 should give mean that a .cpt file is recorded every minute,
> but
> >> no file is found in the directory where I run the script from. mdrun
> works
> >> well otherwise.
> >>
> >> I'd appreciate any help.
> >>
> >>
> > Energy minimization doesn't produce checkpoint files.  There's no point -
> > there are no velocities or state variables to save.
> >
> > -Justin
> >
> > --
> > ==================================================
> >
> > Justin A. Lemkul, Ph.D.
> > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >
> > Department of Pharmaceutical Sciences
> > School of Pharmacy
> > Health Sciences Facility II, Room 629
> > University of Maryland, Baltimore
> > 20 Penn St.
> > Baltimore, MD 21201
> >
> > jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> > http://mackerell.umaryland.edu/~jalemkul
> >
> > ==================================================
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>
>
> --
> Yonatan Zelnik
> yonatanzelnik at gmail.com
> 408.644.3931
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