[gmx-users] rdf

[David van der Spoel]

On Wed, 2004-06-23 at 09:50, nicolas Dinter wrote:
> David,
> 
> I allready set nrexcl to 5, but I still have such results.
Is this a C-C rdf? it should only give a peak at 0.5 nm or so
> 
> nicolas dinter
> 
> -----Original Message-----
> From: gmx-users-bounces at gromacs.org
> [mailto:gmx-users-bounces at gromacs.org]On Behalf Of David van der Spoel
> Sent: mercredi 23 juin 2004 16:39
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] rdf
> 
> 
> 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
> >
> > _______________________________________________
> > gmx-users mailing list
> > gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> --
> David.
> ________________________________________________________________________
> 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
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
-- 
David.
________________________________________________________________________
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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++