Hi, I am interested in obtaining temperature readings that are corrected for velocity (meaning, if a molecule has a net velocity, that kinetic energy should not be counted as part of temperature). I suspect this is what the traj -mol option would do, but I can't get it to run without error.
I am guessing the problem lies with my index files. The traj docs state that "When -mol is set, the numbers in the index file are interpreted as molecule numbers...". I don't understand this. All my index files contain are group headings and atom numbers. It seems like there would need to be another column that indicates molecule number (and I know such a column exists in some other file formats, but nothing I've read indicates that .ndx files can have extra columns). Any idea what I am doing wrong, or can anyone provide a set of test file on which "gmx traj -mol" can be successfully run? Sincerely, James -- 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.
