VMD-L Mailing List

From: Jennifer Williams (Jennifer.Williams_at_ed.ac.uk)
Date: Fri Sep 26 2008 - 09:32:42 CDT

Hi VMD-users,

Sorry if this has already been asked, I couldn't find it in the mailing list.

I am having a visualisation problem when looking at DL_POLY HISTORY
files. When I try and view my structure using bonds, liquorice, CPK or
dynamic bonds representation, I get long bonds stretching across my
entire unit cell as parts of molecules at the edges of the cells move
in and out of the periodic boundary conditions. Basically my molecule
looks like a spiders web because these bonds span the simulation cell
from one end to the other.

The History file doesn't import any information on bonding.

Is there a fix for this? At the moment I am having to use VDW as here
there are no bonds drawn,

Any advice appreciated
Thanks

Jennifer 

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