[gmx-users] PBC in g_gyrate

[Tsjerk Wassenaar]

Hi,

I would say trjconv -pbc cluster sounds more appropriate.

Cheers,

Tsjerk

On 1/17/07, Erik Marklund <erikm at xray.bmc.uu.se> wrote:
> Neither do I, to be honest, but you can always do a trjconv -pbc
> nojump or something similar on your trajectory prior to analysis, just to
> be sure.
> _______________________________________________
> Erik Marklund, PhD student
> Laborarory of Molecular Biophysics,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3,   Box 596,        75124 Uppsala, Sweden
> phone:  +46 18 471 4537         fax: +46 18 511 755
> erikm at xray.bmc.uu.se    http://xray.bmc.uu.se/molbiophys
>
> On Wed, 17 Jan 2007, singh wrote:
>
> >
> >
> > Dear Gromacs users,
> >
> > I simulated 6 peptides in a cubical box. I want to calculate radius of
> > gyration for all the peptides together (in order to get a rough idea whether
> > they are coming together or not). But I am not sure whether g_gyrate takes
> > into account Periodic boundary conditions while calculating radius of
> > gyration for such a system.
> >
> >
> >
> > Regards,
> >
> > Gurpreet Singh
> >
> > -------------------------------------------------
> >
> > University of Dortmund
> > Department of Chemistry
> > Physical Chemistry I  -  Biophysical Chemistry
> > Otto-Hahn Str. 6
> > D-44227 Dortmund
> > Germany
> > Office:   C1-06 room 176
> > Phone:  +49 231 755 3916
> >
> > Fax:     +49 231 755 3901
> >
> > -------------------------------------------------
> >
> >
> >
> >
> _______________________________________________
> 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.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>


-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623