[gmx-users] periodic boundary conditions in g_rdf

Berk Hess gmx3 at hotmail.com
Mon Nov 3 10:20:08 CET 2008


To what value does your rdf go then?

You have pbc in your system, so running with -nopbc is incorrect.
The rdf will then stop at half the box, since you molecules are in the box
and your peptide is probably in the middle, leading to a longest distance
of roughly half the box.


From: ilhan_eins at live.com.mx
To: gmx-users at gromacs.org
Date: Fri, 31 Oct 2008 16:55:54 -0600
Subject: [gmx-users] periodic boundary conditions in g_rdf

Hi everybody.
I'm working a system with a peptide embedded in a lipid bilayer and I try to get the two-dimentional g_rdf for the upper leaflet around the peptide with the -xy option and periodic boundary conditions. But my RDF doesn't go to 1. When a used -nopbc i get almost the same result (just multiplied by a constant) and the RDF is always cutted at the half of size of the box.

Any help will be appreciated.

Thanks in advance.

Conoce el perfil completo de todos tus amigos de Windows Live Messenger justo aquí: Windows Live Spaces

Express yourself instantly with MSN Messenger! Download today it's FREE!
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20081103/897e578a/attachment.html>

More information about the gromacs.org_gmx-users mailing list