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? Many thanks in advance Anu -- 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.