[gmx-users] Bonds missing in VMD visualization [SOLVED]

Andreas Kring akring at fys.ku.dk
Wed Sep 3 13:05:22 CEST 2008

Thank you for solution suggestions!

Solution 1 worked out just fine. After a little Goolgeing it seemed as 
if solution 2 requires modification of the VMD source code. Solution 3 
also looks attractive - I'll have a closer look at this later on...


Diego Enry skrev:
> 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 )
> http://www.ks.uiuc.edu/Research/vmd/allversions/vmd_faq.html
> How to write a .PSF file
> http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/node21.html
> 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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Andreas Kring, Ph.D.-student
University of Copenhagen
Niels Bohr Institute
Universitetsparken 5
DK-2100 Copenhagen

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