[gmx-users] Bonds missing in VMD visualization

Diego Enry diego.enry at gmail.com
Mon Sep 1 16:51:26 CEST 2008

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 <akring at fys.ku.dk> 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
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Diego Enry B. Gomes
Laboratório de Modelagem e Dinamica Molecular
Universidade Federal do Rio de Janeiro - Brasil.

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