[gmx-users] Re: inconsistent energy drops

Justin Lemkul jalemkul at vt.edu
Thu Aug 1 23:01:31 CEST 2013

On 8/1/13 4:58 PM, Brad Van Oosten wrote:
> I used the mdrun -rerun option to recalculate the energies of the system and
> it gave me nearly the same energy plot but without the random drops(see plot
> below).  I am still unsure what is causing the jumps but i do not believe it
> is from my system.  Since the energy is used in the calculation for the next
> step, is there reason to worry about the validity of this run?

Forces dictate the dynamics, not the energies.  This could be either a dynamics 
bug or an output bug.

> potential energy (black being the original potential and red being the
> -rerun)
> <http://gromacs.5086.x6.nabble.com/file/n5010294/pot_rerun.png>
> Zoomed in on first peaks:
> <http://gromacs.5086.x6.nabble.com/file/n5010294/pot_rerun_close.png>

OK, that does look weird.  What Gromacs version is this?  What is in your .mdp file?



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 | (410) 706-7441


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