[gmx-users] including non standard amino acid CSD in topology file

hello I am using OPLS AA FF and my protein contains a non standard amino acid CSD for which the topology parameters are not present . Can someone tell how to include CSD into topology file? ashu -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-u

Re: [gmx-users] including non standard amino acid CSD in topology file

.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

[gmx-users] performance issue with the parallel implementation of gromacs

am doing wrong or how can I decrease the simulation time. -- Regards Ashutosh Srivastava -- gmx-users mailing listgmx-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! * Ple

Re: [gmx-users] performance issue with the parallel implementation of gromacs

is used and > not the Ethernet? It could also be that a single process is still > running on any of your cores and eating up CPU time. Or maybe the > pinning of threads to cores is not correct (what does md.log say > about that?). > > Just a few ideas. > > Good luck! > &g