Re: [gmx-users] log file not writing simulation time in continuous manner
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 = 250 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 = 1.01.0 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*0.0 * 0.0 Energies (kJ/mol) BondU-BProper Dih. Improper Dih. CMAP Dih. 2.70981e+041.28824e+059.76982e+042.20959e+032.96128e+02 LJ-14 Coulomb-14LJ (SR) Coulomb (SR) Coul. recip. 1.93530e+04 -3.84842e+047.57381e+04 -1.87856e+067.47371e+03 Position Rest. Dih. Rest. PotentialKinetic En. Total Energy 1.93759e+030.0e+00 -1.55642e+064.40783e+05 -1.11564e+06 Temperature Pressure (bar) Constr. rmsd 3.03457e+022.41812e+023.91153e-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*2.0*0.0 Energies (kJ/mol) BondU-BProper Dih. Improper Dih. CMAP Dih. 2.70890e+041.29741e+059.79287e+042.28826e+032.58526e+02 LJ-14 Coulomb-14LJ (SR) Coulomb (SR) Coul. recip. 1.94561e+04 -3.80345e+047.15659e+04 -1.87484e+067.69793e+03 Position Rest. Dih. Rest. PotentialKinetic En. Total Energy 2.00424e+030.0e+00 -1.55485e+064.41080e+05 -1.11377e+06 Temperature Pressure (bar) Constr. rmsd 3.03661e+021.71385e+023.91311e-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.
Re: [gmx-users] log file not writing simulation time in continuous manner
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 = 250 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 = 1.01.0 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*0.0 * 0.0 Energies (kJ/mol) BondU-BProper Dih. Improper Dih. CMAP Dih. 2.70981e+041.28824e+059.76982e+042.20959e+03 2.96128e+02 LJ-14 Coulomb-14LJ (SR) Coulomb (SR) Coul. recip. 1.93530e+04 -3.84842e+047.57381e+04 -1.87856e+06 7.47371e+03 Position Rest. Dih. Rest. PotentialKinetic En. Total Energy 1.93759e+030.0e+00 -1.55642e+064.40783e+05 -1.11564e+06 Temperature Pressure (bar) Constr. rmsd 3.03457e+022.41812e+023.91153e-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*2.0*0.0 Energies (kJ/mol) BondU-BProper Dih. Improper Dih. CMAP Dih. 2.70890e+041.29741e+059.79287e+042.28826e+03 2.58526e+02 LJ-14 Coulomb-14LJ (SR) Coulomb (SR) Coul. recip. 1.94561e+04 -3.80345e+047.15659e+04 -1.87484e+06 7.69793e+03 Position Rest. Dih. Rest. PotentialKinetic En. Total Energy 2.00424e+030.0e+00 -1.55485e+064.41080e+05 -1.11377e+06 Temperature Pressure (bar) Constr. rmsd 3.03661e+021.71385e+023.91311e-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
