I'm interested carrying out a long simulation of a thin, narrow protein. Clearly, the volume-minimizing way to do this would be to put it in a thin, narrow box of solvent. The issue with this is that it could rotate around and interact with itself. if the orientation of the protein changed relative to the orientation of the box.
Is there a good way to restrain the orientation in GROMACS currently? I looked a little at the orientation restraint for NMR, but it didn't seem like that would really work well (or at least, it was not obvious it would work well), for restraining the overall orientation. Am I missing something? Any other thoughts, suggestions for doing this? Has anyone else done this? Thanks! -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
