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

[Yonatan Zelnik]

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
>
> ==================================================
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>



-- 
Yonatan Zelnik
yonatanzelnik at gmail.com
408.644.3931