[gmx-users] rdf

[David van der Spoel]

On Thu, 2004-06-24 at 02:30, nicolas Dinter wrote:
> 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!
If you are sure that the exclusions work  as advertised (which you can
test by using your normal topology) then you could run g_mindist to
check the shortest distance, and find the atom pairs involved. How about
T-stacking of rings? It could be a H-C distance.
You might also want to look at a C-C rdf.

> 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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> 
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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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++