Thanks Justin for your early response. I was confused about it, but now it's clear. Thanks
--Neeru > Dear Gromacs Users, > > > I have some queries about the parameters in the .mdp file for the pull code. > > If I want to pull my ligand, towards specific atom/group of atoms from > the protein, how am I supposed to mentioned these in the mdp file? > > ***************************************************************** > pull = umbrella > pull_geometry = distance > pull_start = yes > pull_ngroups = 1 > pull_group0 = Ligand > pull_group1 = Atom/group of atoms from the protein > ***************************************************************** > > Here, I want to specify the pull_group0 as "Ligand" and pull_group1 as > "Atoms of the protein". My query is regarding these groups. Shall I > just write the name of the Ligand and Atoms (specifying the atom no) > or am I supposed to create a separate index file for each of them (one > for ligand and other for group of atoms) ? > All groups specified in the .mdp file must be either valid default groups or custom groups provided in an index file. -Justin -- 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
