From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Thu Apr 17 2008 - 11:07:27 CDT

2008/4/16 cong chen <vmd_chcwaaa_at_yahoo.com.cn>:
> Dear all,
> I want to calculate inter-molecular radial distribution function. For
> glycerol, the first selection is "name C" and I want to select the "O" atoms
> which is NOT in the same molecule as "C". Then what's the text for select2?
> I would be grateful if someone could give me any advice.

the gofr plugin cannot handle this 'as is' since it has
no knowledge of what is a molecule and not. it only sees atoms.
adding an option to exclude the same (residue/chain/segment)
would require some programming effort (feel free to contribute).
moreover it would require a careful rethinking of the normalization.

however, have you checked whether the peaks for the intramolecular
and intermolecular peaks do overlap? if not, you can just go ahead and
then simply disregard the intramolecular peaks...

cheers,
    axel.
>
>
>
> ________________________________
> Ż䣬䣡

-- 
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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.