[gmx-users] rdf

[nicolas Dinter]

David,

I allready set nrexcl to 5, but I still have such results.

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.