Hi Peter, > Instead of the pairs with the shortest distance a much further pair is > selected. Although the output pair from "atm-pair.out" has a distance of more > then 100 Angstrom the value in the file "mindist.xvg" is smaller then one > Angstrom.
Periodic Boundary Conditions? You mention in another post that removing the header solves your 'bug'. The way you express yourself indicates you haven't got a clue what you've removed. Dangerous... Bad idea. You've probably removed a line which started with CRYST1, preceded by a line REMARK This is a simulation box, or something along those lines. Sure, if you remove PBC that way, no gromacs utility will ever see that things should be close to each other. But you're the one that's mistaken, not the program. Don't let yourself be mislead by visualization programs. Hope it helps, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist -- 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/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/mailing_lists/users.php
