VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Tue Apr 22 2008 - 10:10:35 CDT

On Tue, 22 Apr 2008, cipitaua_at_gmail.com wrote:

RC> Hello,
RC>
RC> I noticed that the first peak of a g(r) calculation with the vmd
RC> extension is slightly shifted respect to the expected value.
RC> Check this out with a very well ordered structure (for example
RC> graphene).
RC> In my case (cristalline silicon nanoclusters) it gives 2.70 instead of
RC> 2.43.
RC>
RC> Anyone confirms?

no. the peaks are exactly where they should be in my tests.
e.g. in rigid spc/e water it get the intramolecular peak at
exactly 1. angstrom.

please provide a coordinate/trajectory file that reproduces this,
explain how you obtained it, and with which code you get the
different g(r).

thanks,
   axel.

RC>
RC> Thanx,
RC> Rob.
RC> 

-- 
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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.