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

Justin Lemkul jalemkul at vt.edu
Wed Feb 26 17:14:56 CET 2014

On 2/26/14, 10:50 AM, gupta.rakesh082 wrote:
> I am using gromacs 4.6.5. Surprisingly system is stable at such high
> potential energy. I created bilayer system using packmol then solvated it
> with water using genbox.
> I did energy minimization using following command
> grompp -f em.mdp -c cerblayer.gro -p cer.itp -o min.tpr
> mdrun -c -v -deffnm min
> The resulted potential energy of system was negative (~ 2x 10^-5 ).
> Then I performed NPT run using following command
> grompp -f NPT.mdp -c min.gro -p cer.itp -o NPT.tpr
> mdrun -c -v -deffnm NPT
> The resulted structure and system was stable but the potential energy of
> the system was highly positvie (~ 10^5).

Do you see a massive expansion of box vectors during NPT?  Such a net repulsive 
potential should cause the system to expand quite dramatically.

> Just for curiosity I took resulted NPT.gro structure and ran NPT simulation
> on my desktop which has same version of GROMACS (same precision).
> Surprisingly the total energy was negative after few ps run and converse to
> around order of ~ -10^5.
> I have attached my input .mdp files for energy minimization and NPT MD run.

The list doesn't accept attachments.  You can just copy and paste their 
contents.  The .mdp files are less critical than actual screen output from:

1. Energy minimization (Epot, Fmax, etc)
2. The output of g_energy on npt.edr (Potential energy with RMSD, box vectors, 
and anything else you are examining)

You've got some inconsistencies in notation above that I am assuming are typos, 
but to be 100% we are on the same page, I need to see the exact 
(copied-and-pasted-from-terminal) output that you are getting.



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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