VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Fri Sep 26 2008 - 11:46:39 CDT

On Fri, 26 Sep 2008, Jennifer Williams wrote:

hi jennifer,

JW> Hi VMD-users,
JW>
JW> Sorry if this has already been asked, I couldn't find it in the mailing
JW> list.
JW>
JW> I am having a visualisation problem when looking at DL_POLY HISTORY files.
JW> When I try and view my structure using bonds, liquorice, CPK or dynamic
JW> bonds representation, I get long bonds stretching across my entire unit cell
JW> as parts of molecules at the edges of the cells move in and out of the
JW> periodic boundary conditions. Basically my molecule looks like a spiders web
JW> because these bonds span the simulation cell from one end to the other.

this is the typical behavior when your MD code does
"wrap" atom coordinates back into the principle unit cell.
VMD analyses the bond structure only once (or reads it from
a file with topology information, e.g. a .psf file) and then
maintains this information regardless of where your atoms go.

JW> The History file doesn't import any information on bonding.
JW>
JW> Is there a fix for this? At the moment I am having to use VDW as here there
JW> are no bonds drawn,

there are multiple ways to address this problem. you can use the
PBCtools plugin to "join" bonds stretching across the pbc and/or
to "unwrap" the trajectory again. see:
http://www.ks.uiuc.edu/Research/vmd/plugins/pbctools/

a second option would be to play with the "Dynamic Bonds"
representation and have bonds recalculated during the
display of the trajectory. you can emulate a licorice type
display by combining a dynamic bonds representation for
"all" with a cutoff of ~1.2 AA (to get all bonded hydrogens),
a second dynamic bonds representations with a cutoff of ~1.6
and a selection 'not hydrogen' to get all C-C, C-N, C-O and
related bonds and a VDW representation for "all" with the
radius set to a small value (~0.2).

cheers,
   axel.

JW>
JW> Any advice appreciated
JW> Thanks
JW>
JW> Jennifer
JW>
JW>
JW> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.