I ran the following for the minimization using mpich2: mpiexec -n 8 mdrun_mpi -s min.tpr -c min.gro -o min.trr -g min.log -e min.edr
On Fri, Oct 17, 2008 at 12:36 PM, David van der Spoel <[EMAIL PROTECTED]> wrote: > Lillian Chong wrote: >> >> Dear Gromacs Users, >> >> When I run a steepest descent minimization with the parallel version >> of mdrun in Gromacs 4, it runs to completion (all 1000 steps), but >> does not exit. See below for the tail end of the log file (notice >> there are not timings and the usual Gromacs quote at the end). The >> serial version of the Gromacs 4 mdrun runs this minimization fine and >> exits as it should. I did not have this issue with the Gromacs4rc3 >> parallel mdrun. Do you know what might be going wrong? > > Which mpi version are you using? >> >> I've attached the min.mdp and min.tpr files. >> >> Best regards, >> Lillian >> ==================== >> Tail end of log file: >> Step Time Lambda >> 1000 1000.00000 0.00000 >> >> Energies (kJ/mol) >> Bond Angle Proper Dih. Ryckaert-Bell. LJ-14 >> 2.75995e+01 1.01358e+02 5.12660e+00 1.82811e+02 2.18810e+02 >> Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. >> 8.24670e+02 1.97157e+04 -9.79168e+02 -1.44989e+05 -1.75892e+04 >> Potential Pressure (bar) >> -1.42482e+05 1.42736e+04 >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php > > > -- > David. > ________________________________________________________________________ > David van der Spoel, PhD, Professor of Biology > Dept. of Cell and Molecular Biology, Uppsala University. > Husargatan 3, Box 596, 75124 Uppsala, Sweden > phone: 46 18 471 4205 fax: 46 18 511 755 > [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php > -- Lillian T. Chong Assistant Professor Department of Chemistry University of Pittsburgh 219 Parkman Avenue Pittsburgh, PA 15260 (412) 624-6026 _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php