[gmx-users] the effect of "nexcl" on the result of g_rdf

David van der Spoel spoel at xray.bmc.uu.se
Mon Oct 12 16:16:02 CEST 2009

wuxiao wrote:
> Dear GMXers,
>    I have a bit puzzle about the use of nexcl. In order to calculate the 
> intermolecular g_rdf, the tpr file obtained from a top file is provided 
> with the option -s. So the nexcl in the top file would effect the result 
> of g_rdf. Suppose the nexcl is 3, whether are the two atoms seperated by 
> 3 bonds as a pair included into the calculation of the routin g_rdf? 
> Please ensure me the truth. Thanks a lot for any reply to this post.

If you e.g.have benzene, C6H6, and only want the intermolecular part of
the RDF then you have to set the nrexcl to 5.
For ethane the number would have to be 3. You start counting from the
central atom at zero.

Don't use the same tpr for simulations though.

> Sincerely,
> Chaofu Wu, Dr 
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David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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