VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Tue Mar 25 2008 - 22:56:27 CDT

On Tue, 25 Mar 2008, Krishnan, Marimuthu wrote:

KM> Hello,

hi,
  
KM> I would like to calculate reorientational time correlation function
KM> (second order Legendre polynomial form) of a bond vector (say,
KM> connecting atoms A and B). Is there a tcl script available for this

not that i know of.

KM> purpose? I have written a fortran90 code for this but I have a
KM> feeling that vmd/tcl script can be efficient than my code! Since I

not as far as the calculation of the correlation function goes.
the best compromise would be to compile a plugin that can be
fed a list of vectors (as a time series) which are computed
with tcl script. the advantage is the flexibility of VMD scripting
and particularly selections to pick coordinates of interest.

KM> am a newbie with VMD, I would appreciate if someone could help me in
KM> this. Thanks.

there are several issues connected. there is a lot of related
material referred to on the VMD tutorial pages. i recommend
to have a look at that first. as for writing a plugin i could
send you the code for a plugin to compute radial distribution
functions (before it was integrated into "measure") as a
starting point. it is moderately commented so it would help.

mapping fortran90 would be a bit challenging, but not impossible
if SWING supports it...

cheers,
   axel.
  
KM> cheers,
KM> Krishnan
KM>
KM> *************************************************
KM>
KM> Marimuthu Krishnan
KM> Center for Molecular Biophysics,
KM> Oak Ridge National Laboratory,
KM> PO Box 2008 MS6164,
KM> Oak Ridge, TN 37831-6164,
KM> Tel : 001-865-574-6123
KM> Fax : 001-865-576-7651
KM> E-mail : krishnanm_at_ornl.gov
KM>
KM> *************************************************
KM> 

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