<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><br><div><div>22 mar 2012 kl. 08.05 skrev lina:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>On Wed, Mar 21, 2012 at 11:36 PM, Kukol, Andreas <<a href="mailto:a.kukol@herts.ac.uk">a.kukol@herts.ac.uk</a>> wrote:<br><blockquote type="cite">Hello,<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Upon continuing a replica exchange MD simulation using the command<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">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<br></blockquote><br><blockquote type="cite">From my side, I have no problem resuming or extending the REMD<br></blockquote>simulations in V.4.5.5 and 4.5.4<br></div></blockquote><div><br></div>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.</div><div><br></div><div>Erik</div><div><br><blockquote type="cite"><div><br>Here is the command:<br><br>mdrun_g_f -s md_.tpr -multi 32 -replex 500 -cpi state_.cpt -append<br><br> ^^^^^^^^ I use state_.cpt, not state.cpt<br><br><blockquote type="cite"><br></blockquote><blockquote type="cite">I get the following output:<br></blockquote><blockquote type="cite">**************************************<br></blockquote><blockquote type="cite">...<br></blockquote><blockquote type="cite">...<br></blockquote><blockquote type="cite">5000000 steps, 10000.0 ps (continuing from step 49430, 98.9 ps).<br></blockquote><blockquote type="cite">5000000 steps, 10000.0 ps (continuing from step 49430, 98.9 ps).<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">step 49430, will finish Wed Sep 12 16:09:33 2012<br></blockquote><blockquote type="cite">step 50000, will finish Thu May 24 11:23:04 2012<br></blockquote><blockquote type="cite">Step 47546: resetting all time and cycle counters<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">=>> PBS: job killed: walltime 604823 exceeded limit 604800<br></blockquote><blockquote type="cite">Terminated<br></blockquote><blockquote type="cite">******************************************<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">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.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Also the log-file does not show any more steps:<br></blockquote><blockquote type="cite">************************************************<br></blockquote><blockquote type="cite"> Step Time Lambda<br></blockquote><blockquote type="cite"> 46455 92.91000 0.00000<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Grid: 18 x 17 x 25 cells<br></blockquote><blockquote type="cite"> Energies (kJ/mol)<br></blockquote><blockquote type="cite"> G96Angle Proper Dih. Ryckaert-Bell. Improper Dih. LJ-14<br></blockquote><blockquote type="cite"> 5.83095e+04 3.70277e+04 2.14102e+03 8.83853e+03 -7.33070e+02<br></blockquote><blockquote type="cite"> Coulomb-14 LJ (SR) LJ (LR) Disper. corr. Coulomb (SR)<br></blockquote><blockquote type="cite"> 2.29503e+05 3.04138e+05 -2.66781e+04 -8.51221e+03 -2.74692e+06<br></blockquote><blockquote type="cite"> Coul. recip. Position Rest. Potential Kinetic En. Total Energy<br></blockquote><blockquote type="cite"> -9.59421e+05 5.41532e+03 -3.09689e+06 5.18959e+05 -2.57793e+06<br></blockquote><blockquote type="cite"> Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd<br></blockquote><blockquote type="cite"> 2.97550e+02 -1.14933e+02 5.41944e+01 0.00000e+00<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Writing checkpoint, step 49430 at Fri Jan 27 09:43:23 2012<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">-----------------------------------------------------------<br></blockquote><blockquote type="cite">Restarting from checkpoint, appending to previous log file.<br></blockquote><blockquote type="cite">...<br></blockquote><blockquote type="cite">...<br></blockquote><blockquote type="cite">Started mdrun on node 0 Tue Mar 6 16:40:10 2012<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"> Step Time Lambda<br></blockquote><blockquote type="cite"> 49430 98.86000 0.00000<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Grid: 18 x 17 x 25 cells<br></blockquote><blockquote type="cite"> Energies (kJ/mol)<br></blockquote><blockquote type="cite"> G96Angle Proper Dih. Ryckaert-Bell. Improper Dih. LJ-14<br></blockquote><blockquote type="cite"> 5.84241e+04 3.69121e+04 2.09533e+03 8.80916e+03 -4.67086e+02<br></blockquote><blockquote type="cite"> Coulomb-14 LJ (SR) LJ (LR) Disper. corr. Coulomb (SR)<br></blockquote><blockquote type="cite"> 2.29528e+05 2.99825e+05 -2.67028e+04 -8.51334e+03 -2.74410e+06<br></blockquote><blockquote type="cite"> Coul. recip. Position Rest. Potential Kinetic En. Total Energy<br></blockquote><blockquote type="cite"> -9.59506e+05 5.47116e+03 -3.09823e+06 5.18993e+05 -2.57923e+06<br></blockquote><blockquote type="cite"> Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd<br></blockquote><blockquote type="cite"> 2.97570e+02 -1.14963e+02 2.67842e+00 0.00000e+00<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"> Step Time Lambda<br></blockquote><blockquote type="cite"> 50000 100.00000 0.00000<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"> Energies (kJ/mol)<br></blockquote><blockquote type="cite"> G96Angle Proper Dih. Ryckaert-Bell. Improper Dih. LJ-14<br></blockquote><blockquote type="cite"> 5.86161e+04 3.71585e+04 2.15336e+03 8.92946e+03 -4.84684e+02<br></blockquote><blockquote type="cite"> Coulomb-14 LJ (SR) LJ (LR) Disper. corr. Coulomb (SR)<br></blockquote><blockquote type="cite"> 2.29950e+05 3.01014e+05 -2.66724e+04 -8.51306e+03 -2.74349e+06<br></blockquote><blockquote type="cite"> Coul. recip. Position Rest. Potential Kinetic En. Total Energy<br></blockquote><blockquote type="cite"> -9.59537e+05 5.56712e+03 -3.09531e+06 5.19371e+05 -2.57594e+06<br></blockquote><blockquote type="cite"> Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd<br></blockquote><blockquote type="cite"> 2.97787e+02 -1.14956e+02 2.36460e+01 1.50068e-05<br></blockquote><blockquote type="cite">[End of log-file]<br></blockquote><blockquote type="cite">***********************************<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">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.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Many thanks<br></blockquote><blockquote type="cite">Andreas--<br></blockquote><blockquote type="cite">gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br></blockquote><blockquote type="cite"><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br></blockquote><blockquote type="cite">Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br></blockquote><blockquote type="cite">Please don't post (un)subscribe requests to the list. Use the<br></blockquote><blockquote type="cite">www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br></blockquote><blockquote type="cite">Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists">http://www.gromacs.org/Support/Mailing_Lists</a><br></blockquote>--<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!<br>Please don't post (un)subscribe requests to the list. Use the<br>www interface or send it to gmx-users-request@gromacs.org.<br>Can't post? Read http://www.gromacs.org/Support/Mailing_Lists<br></div></blockquote></div><br><div>
<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>-----------------------------------------------</div><div>Erik Marklund, PhD</div><div>Dept. of Cell and Molecular Biology, Uppsala University.</div><div>Husargatan 3, Box 596, 75124 Uppsala, Sweden</div><div>phone: +46 18 471 6688 fax: +46 18 511 755</div><div><a href="mailto:erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</a></div><div><a href="http://www2.icm.uu.se/molbio/elflab/index.html">http://www2.icm.uu.se/molbio/elflab/index.html</a></div></div></span></div></span></span>
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