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) ? Any suggestion is welcome!! Thanks in advance. Neeru -- 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
