Thank you so much for your input, Mark! For some reason I was so focused on turning the constraints off for a group that I couldn't see that I can just imitate the way grompp works and turn on the constraints for the rest of the system. Aiaaah!
-Soren -----Original Message----- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Mark Abraham Sent: Wednesday, September 23, 2009 3:51 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] all-bonds Enemark Soeren wrote: > Dear GMX-users, > > Is it possible to exclude a group of atoms or molecules from having > their bonds converted to constraints when using the all-bonds mdp-option? Not automatically, but you can edit the topology manually to specify [ constraints ] instead of [ bonds ] for those bonds you wish to be constraints. See chapter 5 for detail. 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 _______________________________________________ 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