Dear GROMACS user, I use the pull code to pull one peptide away from a larger globular protein. For subsequent Umbrella Sampling analyses, I want to keep the peptide within a certain (cylindric, say) volume. However, I want to define the longitudinal axis of the cylider running parallel to the pull direction and the cylinder centered in the box.
The peptide's exact pull path would run approximately near the surface of the cylinder. Is there a way to realize this scenario with the position_restraints directive using flat_bottomed function type? As far as I understand the position_restraint directive, the volume is always centered at the particular atom, which will be restrained. That does not really correspond to my case. Perhaps I'm wrong here. Another way to put it would be having a force acting on the peptide pulling it orthogonal to the original pull direction back to the center longitudinal of the box in an harmonic fashion. I basically want to restrain the volume in the which the peptide is sampled, but the peptide, in its initial conformation is not supposed to be the center of this volume. Thank you very much in advance. Regards -- 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.