Dear Gromacs users, I am trying to run a dPCA to select the best conformation from my trajectory.
When I follow the steps in gromacs manual I have a question about one of the steps: 3. Make an index file <http://www.gromacs.org/Documentation/File_Formats/Index_File>, named as covar.ndx, which necessarily contains one group of atom 1 to integer(2*N/3), where N is the number of dihedral angles. For example, for a peptide of 5 dihedral angles How can I create the covar.ndx? How could I use gmx make_ndx for this? In my case I have 99 atoms and 66 cos/sin integrals. So I guess the covar.ndx should has one group with atoms numbers from 1 2 3 4 5... to 66? Should I have to do this in a text editor by hand? Kindly, Lazaro -- 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.
