[gmx-users] Doubt about energies in a very simple system

Justin Lemkul jalemkul at vt.edu
Thu Feb 26 02:41:23 CET 2015

On 2/24/15 3:23 PM, IÑIGO SAENZ wrote:
> Hi Justin,
> I always do the SPE as follows:
> grompp -f SPE.mdp -p sys.top -c sys.gro
> and after that I simply execute mdrun, i didn't know about the mdrun -rerun
> function.
> Now I have done: mdrun -s topol.tpr -rerun sys.gro
> but the energy results are the exactly the same.

Start with something simpler; an actual molecule with normal bonded 
interactions.  Equivalency of energy between GROMACS and many programs has been 
shown many times over, so it's certainly possible to prove.  Likely there's just 
something weird about what you're doing with your combinations of exclusions, 
pairs, etc.



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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