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

[Justin Lemkul]

On 2/27/14, 2:16 AM, gupta.rakesh082 wrote:
> EM RUN
>
> Steepest Descents converged to machine precision in 2820 steps,
> but did not reach the requested Fmax < 10.
> Potential Energy  = -2.9268122e+05
> Maximum force     =  1.9479546e+02 on atom 123
> Norm of force     =  6.3931437e+00
>
> grompp -f em.mdp -c cerblayer.gro -p cer.itp -o min.tpr
> mdrun -c -v -deffnm min
>
> g_energy -f min.edr -o npt_potenital.xvg
> 10 0
>
> Statistics over 2818 steps [ 0.0000 through 2817.0000 ps ], 1 data sets
> All statistics are over 2225 points (frames)
>
> Energy                      Average   Err.Est.       RMSD  Tot-Drift
> -------------------------------------------------------------------------------
> Potential                   -287434       2800    6986.15   -18110.5
> (kJ/mol)
>
>
>
> NPT RUN
>
> grompp -f NPT.mdp -c min.gro -p cer.itp -o NPT.tpr
> mdrun -nt 8 -c -v -deffnm NPT
>
> g_energy -f NPT.edr -o npt_potenital.xvg
> 10 0
>
> Statistics over 10000001 steps [ 0.0000 through 20000.0000 ps ], 1 data sets
> All statistics are over 100001 points
>
> Energy                      Average   Err.Est.       RMSD  Tot-Drift
> -------------------------------------------------------------------------------
> Potential                    168770       1300    31030.1   -6644.57
> (kJ/mol)
>
> I am surprised to see that at such huge potential energy my simulation box
> is still stable.
>
> Desktop Run
>
> I took generated NPT.gro file in previous run and performed a small 200 ps
> npt simulation on my desktop machine using following commmand.
>
> grompp -f NPT.mdp -c NPT.gro -p cer.itp -o NPTdesktop.tpr
> mdrun --c -v -deffnm NPTdesktop
>
> g_energy -f NPTdesktop.edr -o NPTdesktop_potential.xvg
>
> Statistics over 100001 steps [ 0.0000 through 200.0000 ps ], 1 data sets
> All statistics are over 1001 points
>
> Energy                      Average   Err.Est.       RMSD  Tot-Drift
> -------------------------------------------------------------------------------
> Potential                   -234831         47    582.555    117.566
> (kJ/mol)
>
> This time potential energy became negative after few ps and converse to
> value around order of ~ -2x 10^5.
>

Since the run on the cluster is 20,000 ps and the desktop run is only 200 ps, 
the next thing to do is to really compare apples to apples.  What is the 
g_energy output from the first 200 ps of the .edr file from the cluster?  What 
I'm getting at is that perhaps in the longer run, you're simply entering some 
really high energy state over a longer period of time.  The huge net positive 
energy still suggests to me that something isn't stable, because no 
condensed-phase system should have that kind of energy.  The bilayer is fully 
solvated, correct?

-Justin

-- 
==================================================

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
http://mackerell.umaryland.edu/~jalemkul

==================================================