[gmx-users] Bonds missing in VMD visualization

Diego Enry diego.enry at gmail.com
Tue Sep 2 16:59:59 CEST 2008

So I was testing on VMD the C-CL bond distance to draw a bond.
Actually, the limit was a disturbing 1.80A ! So close to the 1.81A you
need :(

Solutions !

1) Use "dynamic bonds representation" and set the cut-off to 1.81 or more

2) Find where VMD sets it's standard cutoff for bonds and set it to
1.81 or more forever.

3) VMD FAQ solution is to make a .PSF (topology) to solve this
problem. ( You will only need the bond list )

How to write a .PSF file

On Tue, Sep 2, 2008 at 5:59 AM, Andreas Kring <akring at fys.ku.dk> wrote:
> 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?
> /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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