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