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
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
