VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Wed May 09 2007 - 07:42:23 CDT

On Wed, 9 May 2007, Joshua D. Moore wrote:

JM> Hi,

josh,

can you please provide more details of what you did and
what goes wrong and ideally upload an example to the
VMD public biocore project BioFS, so that we can try to
reproduce it.

thanks,
   axel.

JM>
JM> I have been using DL_POLY version 3 to create trajectories. When I
JM> visualize, it appears that all of the coordinates are wrapped with the
JM> periodic boundary conditions. So the coordinates of some atoms are not kept
JM> with the molecule (as pbcwrap does with NAMD dcd files). So when bonds are
JM> drawn they are somtimes extended across the box! Is there a way to unwrap
JM> these coordinates? I tried using pbcunwrap from below, but I didn't have
JM> much luck.
JM>
JM> http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/8967.html
JM>
JM> Is there a DL_POLY expert in the list that has already found a way around
JM> this?
JM>
JM> Thanks.
JM>
JM> Josh
JM> 

-- 
=======================================================================
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
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If you make something idiot-proof, the universe creates a better idiot.