VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Fri Aug 01 2008 - 09:27:35 CDT

On Fri, 1 Aug 2008, Bernhard Knapp wrote:

BK> Hi vmd-people
BK>

hi bernhard,

BK> I would like to ask you if there is some kind of modul for vmd which colors
BK> a structure according to a given rmsd-trajectory (created by gromacs)? For a
BK> single structure it would be easy and I would just overwrite the
BK> beta-factors of the pdb file. But if I want to color over a certain time
BK> range according to different rmsds over time it is probably not so easy.
BK> Therefore I wanted to ask you if a modul like this is existing before I
BK> start to write it on my own in TCL.

to do this in VMD you may want to adopt one of the strategies (or a
combination) listed here:

http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/cpmd-vmd/part3.html#chap5_sect3

going through the "user" field is usually the most convenient option.
unfortunately, vmd is missing a convenient way of loading "user" data
during the load of trajectories (it is not so easy to do this in a
generic way).

cheers,
   axel.

BK>
BK> thx and greetings,
BK> Bernhard
BK>
BK> 

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