[gmx-users] gromacs 5.1.2 and a possible bug related to energy minimization step

[Mark Abraham]

Hi,

Indeed, this kind of glitch is intrinsic to writing a cluster of separate
output files. Hopefully we can get energy writing into TNG files and now
there can be enough metadata that users can have a smoother experience.

Mark

On Fri, 1 Apr 2016 14:21 Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 4/1/16 9:01 AM, Brett wrote:
> > Dear All,
> >
> > After running "gmx mdrun -v -deffnm em &", I run "gmx energy -f em.edr
> -o potential.xvg", but xmgrace indicated that the x-axis was "Time (ps)",
> although I think the value indicated by x-axis should be "step".
> >
> > Is it a bug?
> >
>
> Not exactly what I would classify as a "bug" but yes, it should be step, as
> there is no time in energy minimization.  But gmx energy has no way to
> know what
> kind of process was carried out without reading a .tpr file (which for
> almost
> all cases would be irrelevant) so the labeling remains generic.
>
> -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.
>