[gmx-users] rdf

[nicolas Dinter]

David,

I did a benzene-benzene rdf. In my itp file, every atoms are in the same
group, and I've choose to calculate the rdf of 1 gr, selected a group:
1:BNZ, selected a group 1:BNZ.
Effectively I have a pic at 0.5nm but it isn't srong (about 1.2), and more
worring the slope of this pic begins at 0.18nm, that means that there are
benzene at this distance!
Thank you for your help.

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 18:00
To: Discussion list for GROMACS users
Subject: RE: [gmx-users] rdf


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
> >
> > _______________________________________________
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> --
> 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
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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--
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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

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