On 19/04/2010 3:58 PM, 聂雪川 wrote: > Hello gmx-users, > I just have one question about modifing the source code of > gromacs4.0.7.For I want to control the motion of one certain atom (e.g. > atom 200).I added some codes like /"if(n==my_atom)xprime[n][d] = > x[n][d]+...;"/ in the functionstatic /void do_update_md()/ of the file/ > gromacs-4.0.7\src\mdlib\update.c./But when I run it Parallel (mpi run),I > find that the atom serial number n isn't the real atom serial number n > on each CPU.So the code /"if(n==my_atom)"/ is futile.How can I achieve it.
The domain decomposition algorithm defines a mapping from the local state (i.e. subset of topology and atoms) to the global state. You need to harness that, or don't run in parallel. Mark -- 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/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/mailing_lists/users.php
