Hi, I am trying to run US on a system composed of lipid bilayer/ ion/ water/ peptide. The peptide is inserted through the lipid bilayer and I' d like to study the ion conduction through the peptide across the membrane.
In order to do so, I tried to set a specific ion ( Ces with the atom number 85563) as the pull_group1 in mdp file: pull_group1 = Ces_ion So I had to get a new group named Ces_ion contains of Ces 85563. Therefore made a new index file ( index_US.ndx). In this ndx file, there is an extra group in addition of existed groups as this( The last 2 lines in ndx file) : [ system] ... [protein] ... [protein-H] ... [ Ces_ion ] 85563 But after running the grompp, I get this fatal error: File input/output error: index_US.ndx Would you please let me know how I would be able to define a new group for a specific ion ? Did I make a mistake in defining a new group? Would you please give me any suggestions? Thanks in advance, Sincerely, Shima -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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
