the simulations are still running, they should end tomorrow afternoon. Fra
On Tue, 23 Jul 2013, at 06:26 PM, Mark Abraham wrote: > What does gmxcheck have to say about your output files? > On Jul 23, 2013 12:17 PM, "Francesco" <frac...@myopera.com> wrote: > > > Hi all, > > This morning the gpu cluster that I'm using had some troubles with the > > network connection between nodes that deny access to the storage. > > Now, the simulations are still running and it seems that during the > > "shut down" mdrun wrote a lot of checkpoints and restarted the > > simulation once the communication was restored. > > > > Do you think that I will have distortions or errors in the final > > results? > > > > this is a portion of the log file: > > > > ---------------- BEGIN LOG ---------------- > > > > ... > > DD step 46809999 vol min/aver 0.851 load imb.: force 18.2% > > > > Step Time Lambda > > 46810000 93620.00000 0.00000 > > > > Energies (kJ/mol) > > Angle Proper Dih. Improper Dih. LJ-14 > > Coulomb-14 > > 3.29220e+04 3.94888e+04 2.06055e+03 1.69577e+04 > > 1.50705e+05 > > LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. > > Potential > > 3.28228e+05 -2.51293e+04 -3.04153e+06 8.44070e+03 > > -2.48786e+06 > > Kinetic En. Total Energy Temperature Pres. DC (bar) Pressure > > (bar) > > 4.98840e+05 -1.98902e+06 3.10237e+02 -2.13738e+02 > > -4.80807e+01 > > Constr. rmsd > > 2.76295e-05 > > > > Writing checkpoint, step 46813920 at Tue Jul 23 02:45:44 2013 > > Writing checkpoint, step 46813960 at Tue Jul 23 09:48:22 2013 > > Writing checkpoint, step 46814000 at Tue Jul 23 09:48:23 2013 > > Writing checkpoint, step 46814040 at Tue Jul 23 09:48:24 2013 > > Writing checkpoint, step 46814080 at Tue Jul 23 09:48:25 2013 > > ... > > Writing checkpoint, step 46814960 at Tue Jul 23 09:48:44 2013 > > > > > > DD step 46814999 vol min/aver 0.865 load imb.: force 26.2% > > > > Step Time Lambda > > 46815000 93630.00000 0.00000 > > > > Writing checkpoint, step 46815000 at Tue Jul 23 09:48:45 2013 > > > > > > Energies (kJ/mol) > > Angle Proper Dih. Improper Dih. LJ-14 > > Coulomb-14 > > 3.28615e+04 3.93530e+04 1.99727e+03 1.70754e+04 > > 1.51152e+05 > > LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. > > Potential > > 3.30108e+05 -2.51173e+04 -3.04119e+06 8.48412e+03 > > -2.48528e+06 > > Kinetic En. Total Energy Temperature Pres. DC (bar) Pressure > > (bar) > > 4.97562e+05 -1.98772e+06 3.09443e+02 -2.13533e+02 > > 3.68992e+01 > > Constr. rmsd > > 2.70999e-05 > > > > Writing checkpoint, step 46815040 at Tue Jul 23 09:48:46 2013 > > > > ---------------- END LOG ---------------- > > > > thank you for your help > > > > cheers, > > > > Fra > > -- > > Francesco Carbone > > PhD student > > Institute of Structural and Molecular Biology > > UCL, London > > fra.carbone...@ucl.ac.uk > > -- > > gmx-users mailing list gmx-users@gromacs.org > > 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 gmx-users-requ...@gromacs.org. > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > -- > gmx-users mailing list gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Francesco Carbone PhD student Institute of Structural and Molecular Biology UCL, London fra.carbone...@ucl.ac.uk -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
