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...
/Andreas
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 <[EMAIL PROTECTED]> 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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