[gmx-users] difference in potenital energy on desktop and server run

Justin Lemkul jalemkul at vt.edu
Wed Feb 26 11:58:14 CET 2014

On 2/26/14, 12:51 AM, gupta.rakesh082 wrote:
> Dear allI performed MD simulation of lipid bilayer on my desktop it is giving
> correct results and negative potential energy (~ -10^5) but when I ran the
> same simulation on a server using multi thread (-nt 8), It is giving
> positive potential energy (~ 10^5). Initially I thought it might be problem
> with mpi to check this I ran simulation on cluster with single thread but
> still potential energy is positive.Any help would be appreciated

If the potential energy was that high, I would suspect the system crashed - did 
it?  What were you running, EM or MD?  If the latter, did you provide the 
correct, energy-minimized structure to grompp when creating the .tpr file for 
the run?  Detailed commands and actual output would be useful here, otherwise 
it's all guesswork.

Also, what version of Gromacs are you using?



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA 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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