Dear gmx users, A simulation was performed for 50 ns with
; RUN CONTROL integrator = md nsteps = 50000000 dt = 0.001 ; OUTPUT CONTROL nstxout = 1000 nstvout = 1000 nstxtcout = 0 nstlog = 100 nstenergy = 100 The output produced were 0-50.edr, 0-50.trr, 0-50.log, 0-50.pdb state.cpt, state_prev.cpt. The simulation completed normally. After 50 ns, I intend to extend for 4 more ns, write the trajectory file frequently with ; RUN CONTROL integrator = md nsteps = 4000000 dt = 0.001 ; OUTPUT CONTROL nstxout = 00 nstvout = 00 nstxtcout = 10 nstlog = 500 nstenergy = 10 $grompp -f md.mdp -p topol.top -o md50-54.tpr -c 0-50.pdb -n index.ndx $gmxdump -s md50-54.tpr | more md50-54.tpr: inputrec: integrator = md nsteps = 4000000 init_step = 0 ns_type = Grid nstlist = 10 ndelta = 2 nstcomm = 1 comm_mode = Linear nstlog = 500 nstxout = 0 nstvout = 0 nstfout = 0 nstenergy = 10 nstxtcout = 10 init_t = 0 delta_t = 0.001 xtcprec = 1000 nkx = 22 nky = 22 nkz = 40 pme_order = 4 ewald_rtol = 1e-05 ewald_geometry = 0 epsilon_surface = 0 optimize_fft = FALSE ePBC = xyz bPeriodicMols = FALSE bContinuation = FALSE bShakeSOR = FALSE etc = V-rescale epc = Berendsen epctype = Isotropic tau_p = 1 $mdrun_mpi-4.5.5 -s md50-54.tpr -c 50-54.pdb -x 50-54.xtc -e 50-54.edr -g 50-54.log -cpi state.cpt -nice 0 state.cpt is the output of the initial 50ns run. I have used state.cpt to incorporate the velocities frm the initial run. So, I would expect my 2nd simulation to get complete after running for 4 ns. But, that was not the case. I have checked the log file. The time clearly exceeds 4ns. $ tail -15 50-54.log DD step 54500989 load imb.: force 5.6% pme mesh/force 0.429 DD step 54500999 load imb.: force 6.0% pme mesh/force 0.428 Step Time Lambda 54501000 54501.00259 0.00000 Energies (kJ/mol) Bond Angle Proper Dih. Ryckaert-Bell. LJ-14 1.82780e+02 3.37147e+02 8.77788e+01 1.92877e+01 3.90071e+01 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Potential 5.96624e+02 7.91553e+04 -5.73437e+05 -2.73830e+04 -5.20402e+05 Kinetic En. Total Energy Temperature Pressure (bar) 9.75908e+04 -4.22811e+05 2.97855e+02 -5.82198e+01 Kindly suggest what wrong am I doing. and how do I incorporate the velocity from my earlier run. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA
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