[gmx-users] Bonds missing in VMD visualization

Andreas Kring akring at fys.ku.dk
Tue Sep 2 10:59:54 CEST 2008

Thank you for your reply. I tried the following:

> 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.

In 1,1,1-trichloroethane the C-Cl bond distance should be around 1.81A. 
I checked the C-Cl bond distances using g_bond and this give a nice 
Gaussian distribution around 1.81A (which matches what is in the 
topology file).

> 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.

All bond distances are less than 2.0A, but VMD still does not draw a bond?

Is there anything else I can try?


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