From: Θωμας Ευαγγελιδης (te8624_at_mbg.duth.gr)
Date: Mon Aug 06 2007 - 16:52:34 CDT

Hi,
I am writing a plugin for VMD and I need some help. What I am trying to do is to
create dcd files which contain only the atoms that are within a given cutoff
distance from the protein. The problem is that each frame of a dcd must contain
the same number of atoms, so if frame No.1 contains N atoms then I have to find
which N atoms of frame No.2 are closer to the protein and write only them in
the new dcd file. My question is if the "atomselect top "exwithin $cutoff of
protein"" command calculates by default the minimum distance of each atom it
selects from the protein and if there is a way to retrieve it from the source
code. I tried to read the source code but I am not sure if it does what I need.
I just figured out that the "within" macro functions by creating grid cells
enclosing the protein atoms (others) as well as the atoms which souround them
(flgs). I have also some other ideas but that would be the faster way to find
the atoms I need.
I would appreciate any help,
Thomas Evangelidis