VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Thu Jun 12 2008 - 22:24:15 CDT

On Thu, 12 Jun 2008, Nicolas Sapay wrote:

NS> Hello,

nicolas,
 
NS> I want to use PMEpot on a trajectory computed using the OPLS-AA force field
NS> (so charges different from CHARMM). I saw on the graphical it is possible to
NS> load a name/charge map from a *.dat file. Where can I find the
NS> specifications of this format? And is it possible to load this file from the

check out.
http://www.ks.uiuc.edu/Research/vmd/plugins/irspecgui/

the format is rather simple and probably not flexible enough
for what you need. if you have a proper topology file that
VMD can read, it will contain the partial charges and you
don't need to load those explicitly. the three options in
the utility menu are basically "hacks". worst case, you can
write a small script to read in whatever you want and assign
it to the charge field of you atoms.

NS> pmepot command line? (I don't see the option on the pmepot doc page) A last
NS> question: I want do average the potential over the trajectory... Will pmepot
NS> calculate the average potential directly or should I run it on every frame?

see the Avg Frames field. syntax is the same as in the trajectory tab
for graphical representations.

cheers,
   axel.

NS>
NS> Thanks for your help
NS>
NS> Nicolas
NS>
NS> 

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