> I am trying to implement dihedral restraints for lipids in a bilayer > using what is suggested here: > > http://www.gromacs.org/Documentation/How-tos/Dihedral_Restraints > > However, although the dihedral angles seem to be restrained fine, the > leaflets move apart by 10s of nanometers along +z over a nanosecond or > so, after which of course, the simulation crashes. > > Can anyone suggest what I might be doing wrong? > > version 4.5.4 > > In the mdp file: > > ;dihedral restraints > dihre = yes > dihre_fc = 100 > > In the topology: > > [ dihedral_restraints ] > > 17 18 19 20 1 1 100 0 1 2 > 18 19 20 21 1 1 100 0 1 2 > 19 20 21 22 1 1 100 0 1 2 > 20 21 22 23 1 1 100 0 1 2 > 21 22 23 24 1 1 100 0 1 2 > ... > etc. > > Himanshu
Himanshu - I would look for a problem in the atom numbers in your restraints. If something ususual happens (the simulation crashes), then the option works. If it works, the MDP file is most likely correct. The only other candidate is a topology file... Vitaly Dr. Vitaly V. Chaban, 430 Hutchison Hall Dept. Chemistry, University of Rochester 120 Trustee Road, Rochester, NY 14627-0216 THE UNITED STATES OF AMERICA -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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
