Dear gromcas users, I carried out a continuation of previous md run for nsteps of 5000000 and dt of 0.002 using the following commands,
gmx grompp -f md.mdp -o md2.tpr -c md1.gro -t md1.cpt -r ref.pdb -n index.ndx -p topol.top gmx_mpi mdrun -cpi md1.cpt -deffnm md2 The mdp file following run parameters, *************************************************** integrator = md dt = 0.002 nsteps = 5000000 ; nstlog = 1000 nstxout = 0 nstvout = 0 nstfout = 0 nstcalcenergy = 100 nstenergy = 1000 nstxout-compressed = 20000 compressed-x-grps = System ; 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 ; pbc = xyz ; gen_vel = no ; tcoupl = Nose-Hoover tc_grps = Protein POPC CL_SOL tau_t = 0.5 0.5 0.5 ref_t = 305.0 305.0 305.0 ; pcoupl = Parrinello-Rahman pcoupltype = semiisotropic tau_p = 5.0 compressibility = 4.5e-5 4.5e-5 ref_p = 1.0 1.0 ; constraints = h-bonds constraint_algorithm = LINCS continuation = yes ; nstcomm = 100 comm_mode = linear comm_grps = Protein_POPC CL_SOL ; refcoord_scaling = com ************************************************************** Though the run completed successfully, I just noticed from the log file that the simulation carried out only for 3500000 steps, instead of 5000000 steps. It looks to me that the simulation started from the previous run that completed 1500000 steps and the current run went from the next 3500000 steps to complete the total run for 5000000 steps. Why this happened? Why it counted total run as 5000000 steps rather than continue the current for another 5000000 steps? Also, I also noticed that the XTC file is written with 176 frames instead of 175 frames (i.e. 3500000/20000)? Is it writing the last step of the previous run again? Below is the head and tail of the log file. *************************************************** Started mdrun on rank 0 Wed Aug 19 13:21:50 2015 Step Time Lambda 1500000 3000.00000 0.00000 Energies (kJ/mol) Bond U-B Proper Dih. Improper Dih. CMAP Dih. 2.68385e+04 1.29842e+05 9.81752e+04 2.12606e+03 1.22039e+02 LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. 1.92413e+04 -3.79314e+04 8.94538e+04 -2.15678e+06 8.56903e+03 Position Rest. Potential Kinetic En. Total Energy 1.19967e+03 -1.81913e+06 4.40840e+05 -1.37829e+06 Temperature Pressure (bar) Constr. rmsd 3.05915e+02 9.88325e+01 3.99434e-06 DD step 1500024 load imb.: force 23.7% pme mesh/force 0.689 At step 1500025 the performance loss due to force load imbalance is 10.2 % NOTE: Turning on dynamic load balancing DD load balancing is limited by minimum cell size in dimension Z DD step 1500999 vol min/aver 0.797! load imb.: force 2.1% pme mesh/force 1.021 Step Time Lambda 1501000 3002.00000 0.00000 Energies (kJ/mol) Bond U-B Proper Dih. Improper Dih. CMAP Dih. 2.69950e+04 1.30117e+05 9.81626e+04 2.14421e+03 3.04253e+02 LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. 1.92568e+04 -3.91777e+04 8.75313e+04 -2.15233e+06 8.72461e+03 Position Rest. Potential Kinetic En. Total Energy 1.12669e+03 -1.81713e+06 4.39962e+05 -1.37717e+06 Temperature Pressure (bar) Constr. rmsd 3.05306e+02 -1.47275e+02 3.98818e-06 --------------------------------------------- --------------------------------------------- --------------------------------------------- Step Time Lambda 5000000 10000.00000 0.00000 Writing checkpoint, step 5000000 at Wed Aug 19 22:49:38 2015 Energies (kJ/mol) Bond U-B Proper Dih. Improper Dih. CMAP Dih. 2.71898e+04 1.29717e+05 9.78396e+04 2.14084e+03 1.91548e+02 LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. 1.92444e+04 -3.67507e+04 9.10908e+04 -2.16220e+06 8.48970e+03 Position Rest. Potential Kinetic En. Total Energy 1.26666e+03 -1.82178e+06 4.38586e+05 -1.38319e+06 Temperature Pressure (bar) Constr. rmsd 3.04350e+02 7.56441e+01 3.99781e-06 <====== ############### ==> <==== A V E R A G E S ====> <== ############### ======> Statistics over 3500001 steps using 35001 frames Energies (kJ/mol) Bond U-B Proper Dih. Improper Dih. CMAP Dih. 2.71537e+04 1.29908e+05 9.80926e+04 2.22652e+03 1.80928e+02 LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. 1.91048e+04 -3.81235e+04 8.95751e+04 -2.15651e+06 8.65871e+03 Position Rest. Potential Kinetic En. Total Energy 1.19417e+03 -1.81854e+06 4.39526e+05 -1.37901e+06 Temperature Pressure (bar) Constr. rmsd 3.05003e+02 1.27530e+00 0.00000e+00 ********************************************************************************* Many thanks 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.