VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Wed Jul 04 2007 - 11:51:57 CDT

On Tue, 3 Jul 2007, Zhimin Xiong wrote:

hi!

ZX> Hi, all, I am asking for your help when viewing molecular dynamics
ZX> trajectory. For example, I want to display the polymer chain configuration
ZX> from MD trajectory file, however, given the psf file that contains the
ZX> connectivity of the monomer along the chain, some of the bonds cross over
ZX> the box boundary, so the bonds displayed is not true. One way I thought to
ZX> solve it is to view a specific frame of the trajectory file and give the
ZX> connectivity psf file for this frame that don't connect the crossing bonds,
ZX> but it is not convenient to view a lot of frames sequentially. Any
ZX> suggestion is appreciated!

right now i can think of two options that might help you.

1) you can try the DynamicBonds representation. this works best, if
   your bond lengths are rather homogeneous.

2) you can re-apply PBC in a way that only whole molecules are
   subject to box crossings. the PBCtools plugin in VMD should
   be able to help you with that, but also several MD packages
   have tools to handle this or settings to create corresponding
   trajectories.

cheers,
   axel. 

-- 
=======================================================================
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.