VMD-L Mailing List

From: Ignacio Fernández Galván (jellby_at_yahoo.com)
Date: Thu Feb 16 2006 - 05:24:07 CST

Hello,

I have a simulation box where the interesting molecule (the solute) is
near the edge. This poses no problem in the simulation, as it's done
with periodic boundary conditions, and I can enable the periodic images
as well in VMD. The problem is I'm only interested in the molecules
closest to the solute, but if I select them with "within 4 of index 0"
(for example), it only selects the molecules in the "self" cell, but
not in the periodic images (at least, not the ones in the opposite side
of the periodic image, which are actually close the solute).
Graphically, If I have this system:

|ˇˇˇˇ*|ˇˇˇˇ*|
* = solute
| = cell boundary

I want to select this:

|ˇˇˇ##|#ˇˇ##|
# = selected

But I get only this:

|ˇˇˇ##|ˇˇˇ##|

Is there a way to get what I want other than preprocessing the input
file to get it centered around the solute (which would then give the
same problem for other different molecules)?

Thanks

        
        
                
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