Dear Justin, Thanks a lot for your prompt reply.
On Sat, Aug 15, 2015 at 2:55 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 8/15/15 9:51 AM, anu chandra wrote: > >> Dear Gromcas users, >> >> >> I have used grompp, as shown below, to generate .tpr file in order to >> continue the simulation. >> >> gmx_mpi grompp -f md.mdp -o MD5.tpr -c MD4.gro -t MD4.cpt -r ref.pdb -n >> index.ndx -p topol.top >> >> >> My mdp input parameters are shown below, >> >> *************************************************************** >> define = -DPOSRES >> integrator = md >> dt = 0.002 >> nsteps = 2500000 >> nstlog = 1000 >> nstxout = 5000 >> nstvout = 5000 >> nstfout = 5000 >> nstcalcenergy = 100 >> nstenergy = 1000 >> ; >> cutoff-scheme = Verlet >> nstlist = 20 >> rlist = 1.2 >> coulombtype = pme >> rcoulomb = 1.2 >> vdwtype = Cut-off >> vdw-modifier = Force-switch >> rvdw_switch = 1.0 >> rvdw = 1.2 >> ; >> tcoupl = Nose-Hoover >> tc_grps = PROT NPROT SOL_ION >> tau_t = 1.0 1.0 1.0 >> ref_t = 303.15 303.15 303.15 >> ; >> pcoupl = Parrinello-Rahman >> pcoupltype = semiisotropic >> tau_p = 5.0 5.0 >> compressibility = 4.5e-5 4.5e-5 >> ref_p = 1.0 1.0 >> ; >> constraints = h-bonds >> constraint_algorithm = LINCS >> continuation = yes >> ; >> gen-vel = no >> ; >> nstcomm = 100 >> comm_mode = linear >> comm_grps = PROT NPROT SOL_ION >> ; >> refcoord_scaling = com >> >> ******************************************************************* >> >> Unfortunately log file shows simulation time as a new start, not as >> continuation from previous run, as shown below. Time suppose to start from >> 10001 ps. >> >> >> ****************************************************************************************** >> Started mdrun on rank 0 Sat Aug 15 13:15:04 2015 >> Step *Time* Lambda >> 0 *0.00000 * 0.00000 >> >> Energies (kJ/mol) >> Bond U-B Proper Dih. Improper Dih. CMAP >> Dih. >> 2.70981e+04 1.28824e+05 9.76982e+04 2.20959e+03 >> 2.96128e+02 >> LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Coul. >> recip. >> 1.93530e+04 -3.84842e+04 7.57381e+04 -1.87856e+06 >> 7.47371e+03 >> Position Rest. Dih. Rest. Potential Kinetic En. Total >> Energy >> 1.93759e+03 0.00000e+00 -1.55642e+06 4.40783e+05 >> -1.11564e+06 >> Temperature Pressure (bar) Constr. rmsd >> 3.03457e+02 2.41812e+02 3.91153e-06 >> >> DD step 24 load imb.: force 21.2% pme mesh/force 0.689 >> >> At step 25 the performance loss due to force load imbalance is 9.0 % >> >> NOTE: Turning on dynamic load balancing >> >> DD step 999 vol min/aver 0.816 load imb.: force 1.5% pme mesh/force >> 0.768 >> >> Step *Time* Lambda >> 1000 *2.00000* 0.00000 >> >> Energies (kJ/mol) >> Bond U-B Proper Dih. Improper Dih. CMAP >> Dih. >> 2.70890e+04 1.29741e+05 9.79287e+04 2.28826e+03 >> 2.58526e+02 >> LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Coul. >> recip. >> 1.94561e+04 -3.80345e+04 7.15659e+04 -1.87484e+06 >> 7.69793e+03 >> Position Rest. Dih. Rest. Potential Kinetic En. Total >> Energy >> 2.00424e+03 0.00000e+00 -1.55485e+06 4.41080e+05 >> -1.11377e+06 >> Temperature Pressure (bar) Constr. rmsd >> 3.03661e+02 1.71385e+02 3.91311e-06 >> >> ************************************************************************************************* >> >> Can any body help me to figure this out? >> >> > If you continue via grompp, you need to set tinit and init_step to get > continuous output. Continuing via the convert-tpr/mdrun -cpi approach will > continue seamlessly. If you have provided all of the correct inputs to > grompp, the physics is fine; you just need to post-process when > concatenating the trajectories (trjcat -settime). > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > 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. > -- 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.