[gmx-users] Option -shuffle, -sort, -np missing in grompp in version 4.0?
The command grompp used to have options -shuffle, -sort and -np, but it seems that they appear no more with version 4.0? -- Sun Li Department of Physics Nanjing University, China ___ gmx-users mailing listgmx-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
Re: [gmx-users] Option -shuffle, -sort, -np missing in grompp in version 4.0?
Am Samstag, 11. Oktober 2008 schrieb Lee Soin: The command grompp used to have options -shuffle, -sort and -np, but it seems that they appear no more with version 4.0? These options were used for particle decomposition in the tpr file. Gromacs 4 default method is domain decomposition, but as far as I remember, PD is still optional. The options can be set during run-time so that a tpr input file itself is independent of the parallel setup during runtime (the output may depend upon the runtime environement). Thus you should find all options in mdrun. The -np switch isn't required anymore (for mpi). Please correct me if I'm wrong... Best Martin ___ gmx-users mailing listgmx-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
Re: [gmx-users] Option -shuffle, -sort, -np missing in grompp in version 4.0?
Martin Höfling wrote: Am Samstag, 11. Oktober 2008 schrieb Lee Soin: The command grompp used to have options -shuffle, -sort and -np, but it seems that they appear no more with version 4.0? These options were used for particle decomposition in the tpr file. Gromacs 4 default method is domain decomposition, but as far as I remember, PD is still optional. The options can be set during run-time so that a tpr input file itself is independent of the parallel setup during runtime (the output may depend upon the runtime environement). Thus you should find all options in mdrun. The -np switch isn't required anymore (for mpi). Please correct me if I'm wrong... These options have been removed indeed. Domain decomposition is much more efficient than particle decomposition. Therefore PD is useful only in special cases. -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-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
