[gmx-users] rdf

David van der Spoel spoel at xray.bmc.uu.se
Wed Jun 23 09:38:44 CEST 2004

On Wed, 2004-06-23 at 08:50, nicolas Dinter wrote:
> Dear Gromacs users,
> I made a NVT simulation for a 120 rigid benzene, at 293.15K and 1 bar.
> I get stange results from g_rdf witch shows me a raise at 0.18 nm!
> I tryied both g_rdf -com and g_rdf but it was alway bad.
> Every atoms are in the same group, recl=5, and I chose to see 1 group. To me
> it could compute the benzene-benzene rdf.
> Could anyone get any idea?
These are most likely intramolecular peaks. To avoid them you have to
generate a tpr file where all the intramolecular interaction are
excluded, i.e. set nrexcl to 5 and then pass this tpr to g_rdf. 
> Thanks.
> Nicolas Dinter
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone:  +46 18 471 4205  fax: +46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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