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

Justin Lemkul jalemkul at vt.edu
Fri Apr 1 15:21:04 CEST 2016

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 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


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