From: Charlesworth, Henry (
Date: Fri Aug 21 2015 - 07:49:27 CDT

Thanks for the response. Presumably the dynamic bonds representation works by bonding atoms to any other atoms of the selection within the cutoff distance. I guess this would mean you need to do it separately for each polymer otherwise there would be bonds between them. Should be relatively simple but I haven't been using VMD for very long so what would be the command needed to apply that to each resid in a loop?

This is quite a good solution but it seems like it could still be problematic, as if one part of the polymer comes too close to another part there will be incorrect bonds shown. Is there not any other solution?


From: <> on behalf of Charlesworth, Henry <>
Sent: 20 August 2015 18:44
Subject: vmd-l: removing bonds across periodic boundary in a video


I have a system which is a graphene sheet and a polymer melt within a periodic box. I want to make a video with the wrapped coordinates but where bonds across the periodic boundary are not displayed. So far I've found a fix that works for just an image (by removing long bonds) but this is no good for a video where the polymers can move back and forward across the periodic boundary. Does anyone have any suggestions?

Thanks, Henry