VMD-L Mailing List

From: Jim Shepherd (jimshep_at_mindspring.com)
Date: Mon Apr 26 2004 - 14:19:02 CDT

I am trying to use VMD to display a polymer network in which molecules
exit one face of the periodic box and re-enters on the opposite face.
The structure and atoms locations are being imported from PSF and PDB
files and all of the atoms are within the periodic box. When displaying
the molecules in VMD, the bonds connecting atoms that would be on
opposite sides of the periodic box are drawn across the box (the
displayed bond length is equal to the PB size minus the actual bond
length). I have searched the mailing list archives, read the user
manual and FAQ, and searched google without finding any definite
solutions.

I tried using the dynamic bond drawing method, but it frequently draws
bonds between adjacent, non-bonded atoms. It looks like I may be able
to delete these bods by using scripts, but I am not sure what the best
approach would be. Should I use the atomselect command to find all the
bonds and then remove bonds that are longer than some threshold?

-Jim Shepherd