[gmx-users] question about periodic boundary conditions

[rainy908 at yahoo.com]

Hi,

Is there a way to quantitatively determine, from a trajectory file, whether
a molecule is interacting with a copy of itself in the adjacent box (given
that PBC is applied)?  Currently, I'm using VMD - I've already loaded the
*xtc file into the*gro structure file and viewed the "periodic images to
draw" under the Periodic tab of Graphical Representations.

But I figure there's got to be an analytical way to do this, using g_dist or
g_mindist?  How the molecule is interacting (with its adjacent copy) is not
the primary interest - I just want to know whether interactions among
adjacent molecules are occurring.

Does anyone have any ideas?

Thanks,
Lili
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20101020/7a0bdf52/attachment.html>