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 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
