Well, I thought that it would work for for freeze groups, and that is what I intended to say. I've used freeze groups before, but don't have tonnes of experience with them. The gromacs mdp options page reads as if it should work ( http://manual.gromacs.org/online/mdp_opt.html#neq ), but if Justin says that you can not use an index group for freeze groups (only position restraints) then I suggest that you take his word for it. He answers a lot more posts and is probably more familiar with the ins and outs of gromacs.
Chris,. -- original message -- Alex Marshall amarsh59 at uwo.ca Wed Oct 31 20:55:08 CET 2012 Previous message: [gmx-users] Freeze group atoms changing position Next message: [gmx-users] Freeze group atoms changing position Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] Chris, is that for freeze groups or position restraints? On Wed, Oct 31, 2012 at 3:22 PM, Christopher Neale < chris.neale at mail.utoronto.ca> wrote: > No need to rename... just make an .ndx group. > > -- original message -- > > As I understand it, position restraints for an atom are set in the topology > file and applied to that atom in each of that species. In order to restrain > some but not all of the water I'd have to copy the topology of my water > model and add the restraints, then rename (and group together) the atoms I > want to freeze so that they're identified with the appropriate topology > file. Does this sound like it would work? Is there some other way that you > might do it? > > Thanks > -- 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/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 http://www.gromacs.org/Support/Mailing_Lists
