22 mar 2012 kl. 08.05 skrev lina: > On Wed, Mar 21, 2012 at 11:36 PM, Kukol, Andreas <[email protected]> wrote: >> Hello, >> >> Upon continuing a replica exchange MD simulation using the command >> >> mdrun -cpi state.cpt -append -s tpr_remd20ns_.tpr -multi 48 -replex 10000 >> -cpt 60 -x xtcRemd_20ns.xtc -c afterRemd_20ns.gro -g logRemd_20ns.log -v -e >> edrRemd_20ns.edr -stepout 2000 > >> From my side, I have no problem resuming or extending the REMD > simulations in V.4.5.5 and 4.5.4
I've had problems with continuation of REMD simulations with gmx 4.5.5 (although manifested differently IIRC). The release-4-5-patches contain bugfixes that solved the problems. I suggest trying the patches. Erik > > Here is the command: > > mdrun_g_f -s md_.tpr -multi 32 -replex 500 -cpi state_.cpt -append > > ^^^^^^^^ I use state_.cpt, not state.cpt > >> >> I get the following output: >> ************************************** >> ... >> ... >> 5000000 steps, 10000.0 ps (continuing from step 49430, 98.9 ps). >> 5000000 steps, 10000.0 ps (continuing from step 49430, 98.9 ps). >> >> step 49430, will finish Wed Sep 12 16:09:33 2012 >> step 50000, will finish Thu May 24 11:23:04 2012 >> Step 47546: resetting all time and cycle counters >> >> =>> PBS: job killed: walltime 604823 exceeded limit 604800 >> Terminated >> ****************************************** >> >> Apparently, the job runs for one week on a computer cluster (that is the >> maximum time allowed), but it does not progress very much beyond step 49430. >> >> Also the log-file does not show any more steps: >> ************************************************ >> Step Time Lambda >> 46455 92.91000 0.00000 >> >> Grid: 18 x 17 x 25 cells >> Energies (kJ/mol) >> G96Angle Proper Dih. Ryckaert-Bell. Improper Dih. LJ-14 >> 5.83095e+04 3.70277e+04 2.14102e+03 8.83853e+03 -7.33070e+02 >> Coulomb-14 LJ (SR) LJ (LR) Disper. corr. Coulomb (SR) >> 2.29503e+05 3.04138e+05 -2.66781e+04 -8.51221e+03 -2.74692e+06 >> Coul. recip. Position Rest. Potential Kinetic En. Total Energy >> -9.59421e+05 5.41532e+03 -3.09689e+06 5.18959e+05 -2.57793e+06 >> Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd >> 2.97550e+02 -1.14933e+02 5.41944e+01 0.00000e+00 >> >> Writing checkpoint, step 49430 at Fri Jan 27 09:43:23 2012 >> >> ----------------------------------------------------------- >> Restarting from checkpoint, appending to previous log file. >> ... >> ... >> Started mdrun on node 0 Tue Mar 6 16:40:10 2012 >> >> Step Time Lambda >> 49430 98.86000 0.00000 >> >> Grid: 18 x 17 x 25 cells >> Energies (kJ/mol) >> G96Angle Proper Dih. Ryckaert-Bell. Improper Dih. LJ-14 >> 5.84241e+04 3.69121e+04 2.09533e+03 8.80916e+03 -4.67086e+02 >> Coulomb-14 LJ (SR) LJ (LR) Disper. corr. Coulomb (SR) >> 2.29528e+05 2.99825e+05 -2.67028e+04 -8.51334e+03 -2.74410e+06 >> Coul. recip. Position Rest. Potential Kinetic En. Total Energy >> -9.59506e+05 5.47116e+03 -3.09823e+06 5.18993e+05 -2.57923e+06 >> Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd >> 2.97570e+02 -1.14963e+02 2.67842e+00 0.00000e+00 >> >> Step Time Lambda >> 50000 100.00000 0.00000 >> >> Energies (kJ/mol) >> G96Angle Proper Dih. Ryckaert-Bell. Improper Dih. LJ-14 >> 5.86161e+04 3.71585e+04 2.15336e+03 8.92946e+03 -4.84684e+02 >> Coulomb-14 LJ (SR) LJ (LR) Disper. corr. Coulomb (SR) >> 2.29950e+05 3.01014e+05 -2.66724e+04 -8.51306e+03 -2.74349e+06 >> Coul. recip. Position Rest. Potential Kinetic En. Total Energy >> -9.59537e+05 5.56712e+03 -3.09531e+06 5.19371e+05 -2.57594e+06 >> Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd >> 2.97787e+02 -1.14956e+02 2.36460e+01 1.50068e-05 >> [End of log-file] >> *********************************** >> >> I wonder, if this is my mistake (using the mdrun wrongly), a Gromacs problem >> or maybe a problem of the computer cluster (MPI, etc). I would be grateful >> for any help. >> >> Many thanks >> Andreas-- >> gmx-users mailing list [email protected] >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to [email protected]. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists ----------------------------------------------- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: +46 18 471 6688 fax: +46 18 511 755 [email protected] http://www2.icm.uu.se/molbio/elflab/index.html
-- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
