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
[EMAIL PROTECTED] 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
-------------------------------------------------
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