[gmx-users] difference in potenital energy on desktop and server run
gupta.rakesh082 at gmail.com
Wed Feb 26 16:54:32 CET 2014
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).
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.
On Wed, Feb 26, 2014 at 4:41 PM, Justin Lemkul [via GROMACS] <
ml-node+s5086n5014819h17 at n6.nabble.com> wrote:
> On 2/26/14, 12:51 AM, gupta.rakesh082 wrote:
> > Dear allI performed MD simulation of lipid bilayer on my desktop it is
> > correct results and negative potential energy (~ -10^5) but when I ran
> > same simulation on a server using multi thread (-nt 8), It is giving
> > positive potential energy (~ 10^5). Initially I thought it might be
> > with mpi to check this I ran simulation on cluster with single thread
> > 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
> the run? Detailed commands and actual output would be useful here,
> 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
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