VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Mon May 08 2006 - 11:46:49 CDT

On Mon, 8 May 2006, Guo Zhi wrote:

GZ> Well, my system is NPT. I want to use "measure minmax [atomselect top
water]" to calculate the unit cell info in each frame, is this recovery
method correct?

no, your cell will always be too large since molecules will always
be wrapped as a whole.

---------- Forwarded message ----------
From: Guo Zhi <gzgzgz_at_gmail.com>
Date: 2006-5-7 ÏÂÎç11:32
Subject: vmd-l: How to pick up the lost periodic information?
To: vmd-l_at_ks.uiuc.edu

 Hi, VMD users:
      I forgot to include DCDunitCell option in my simulation. So that it
seems that the dcd trajectory file does not include any periodic
information( when i ticked any of the checkbox of +X, -X, +Y, -Y... none of
them works ), but i really want to see the movie with smooth boundary
connected, is it still possible? How to do it?
What's more, how to select neighboring atoms that stride two periodic
boxes?

no, that is currently not possible. you have to duplicate the
atom coordinates accordingly and the analyse.

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