[gmx-users] PBC in g_gyrate

[Erik Marklund]

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
>
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>