VMD computes distances between pairs of atoms to "draw" a bond. So I think your atoms are too distanced from each other. Check the bond distribution during MD and compare with your topology. C-CL should be around 1.76A. VMD will not show this bond if, in the REFERENCE frame (the .gro/pdb you open before the .xtc/.trr), this distance is greater than 2.0A.
On Mon, Sep 1, 2008 at 10:45 AM, Andreas Kring <[EMAIL PROTECTED]> wrote: > Hello, > > I have run an MD simulation of 1000 1,1,1-trichloroethane molecules and it > all worked nicely. But when I try to visualize the trajectory file in VMD > some of the C-Cl bonds are missing (although all the atoms appear on the > screen - only bonds are missing)? > > Can I do anything to fix this? > > /Andreas > _______________________________________________ > gmx-users mailing list [email protected] > http://www.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 [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Diego Enry B. Gomes Laboratório de Modelagem e Dinamica Molecular Universidade Federal do Rio de Janeiro - Brasil. _______________________________________________ gmx-users mailing list [email protected] http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
