VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Fri Jul 27 2007 - 13:26:06 CDT

On Fri, 27 Jul 2007, zhenlong li wrote:

ZL> Dear all,
ZL> As default, atoms crossing the periodical boundaries are wrapped in DCD
ZL> file, this causes problem when only part of a molecule crosses the
ZL> boundary. Is there any easy way to modify the DCD file, so that only whole
ZL> molecules crossing the boundaries will be wrapped? I've tried the unwrap
ZL> command in the pbctools plugin. But the trajectory is still a destroyed one
ZL> since the way of unwrapping is not unique. Thanks in advance!

how about 'pbc wrap -compound seg' or similar?

axel.

ZL>
ZL> best,
ZL> Zhenlong
ZL> 

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