VMD-L Mailing List

From: J. Rui Rodrigues (jrui_at_ci.uc.pt)
Date: Tue Jul 29 2003 - 11:43:23 CDT

Dear vmd-l
In the last few days I've been trying to display some periodic images
and a couple of questions came up...

After setting a,b,c for every frame, when I pick an atom in the "self"
cell or in an image cell, VMD always reports the coordinates from the
self cell.
However, when I set a bond label between atoms in diferent cells, VMD
reports a distance.
Is this distance correct? I mean, am I really getting the distance
between atoms in diferent cells?

Apparently it doesn't seem possible to select atoms in an image cell
within a given distance from an atom in the self cell... but maybe I am
missing something.

How can I calculate the minimum distance between my protein and its
images along a MD trajectory?
Displaying periodic images seemed very promising at first glance, but
unfortunatly it's not taking me to anywhere.
Can you give me any idea of how this could be done?

Thanks,
Rui Rodrigues 

--
J. Rui Rodrigues
Departamento de Química
Faculdade de Ciências e Tecnologia
Universidade de Coimbra
3004-535 Coimbra
Portugal