Hi all, I am trying to add hydrogen bonds to a coarse grained protein model by Ali Ghavami. The model has one bead per amino acid placed at each C-alpha. The model has bending and torsion potentials, and also includes non-bonded interactions like hydrophobicity and electrostatic interactions. (Some beads have charges).
For the hydrogen bonds, the best thing would be to use a directional potential, i.e. the interaction would depend not only on distance, but also on the orientation of both C-alpha's. I was not able to find such a potential for non-bonded interactions in GROMACS however. Does anyone know a way to accomplish this in GROMACS? Any help would be welcome. Wopke -- 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.
