VMD-L Mailing List

From: Florentina Tofoleanu (florentina.tofoleanu_at_gmail.com)
Date: Wed Aug 12 2009 - 07:03:53 CDT

Hello,

I have a question about how VMD "sees" periodic cells. I use periodic
boundaries in my simulations, so when running the resulting .dcd file in
VMD, the molecules that go over the top of my simulation box, I see them at
the bottom of the box(and have negative z coodrinates). When getting the
RMSD for the whole molecular system I get these jumps whenever that happens.

To overcome this, I made this script that adds the Z dimension of the box
whenever the Z coordinate of the jumping molecule is negative and puts then
molecule back to the top. BUT, the molecules reput on the top of the box are
quite distanced from the other molecules that are close to the top but still
in the box. Where does that distance come from and what can I do to get the
jumping molecules at the right coordinate?

Is there any other way of getting rid of the "periodic boundary effect" and
see all my molecules together nicely?

Regards,

Florentina 

-- 
Florentina Tofoleanu
Postgraduate Research Fellow
Theoretical and Computational Biophysics Group
University College Dublin
School of Physics, Rm. 110
Belfield, Dublin 4, Ireland