Dear all, I would like to simulate an elongated ('stretched-out', rod-like) protein in an orthorhombic or tetragonal box to simulate as few solvent particles as possible and save computation time. The longest axis of the protein would be aligned to the box axis with largest side-length.
The problem that I have with this approach is that the protein (obviously) tends to rotate and see its periodic images, once the longest axes of protein and box are no longer aligned. I'm not interested in the rotational diffusion of the protein, so I'm fine with imposing a soft collective restraint on the orientation of the protein to keep it from rotating. I don't want to restrain each atom individually, because that would mess up the dynamics of the protein, but would rather like to impose an energy penalty (harmonic or flat-bottom potential or anything actually), if the vector of the largest principal axis of the inertia tensor deviates by too much from the starting structure. This would allow internal fluctuations to continue happily, as long as the protein does not rotate too much globally. Do you have any idea how to do that in gromacs? I only found an implementation in a hacked older gromacs version from this paper dx.doi.org/10.1021/ct100666v | J. Chem. Theory Comput. 2011, 7, 1381–1393, but I would like to stick with some of the recent gromacs implementations. Thanks and best regards, -- Sören -- 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.