VMD-L Mailing List

From: VISWANADHA SRIDHARA (vsrid001_at_odu.edu)
Date: Thu Sep 08 2005 - 03:38:02 CDT

Hi VMD users,

set number_frames [molinfo top get numframes]
set selection [atomselect top "exwithin 3 of protein"]
for {set i 0} {$i < $number_frames} {incr i} {
   $selection frame i
   $selection update
  set frame_index($i) [$selection get index]
}

This will give the index of the atoms around 3 angst. from protein,
excluding protein atoms, for each frame in the loaded traj., and will save
index values of those select atoms to the array frame_index().
I was wondering how to store this array, and how to use it.
Is it a .dat file?
Can I get the indexes or write indexes of each trajectory(at a particular
time step) into separate file....In other words, can I write indexes at
t=1ps in seperate file, and for t=2ps and so on.
I want to use this information somewhere else.

Best Regards,
-V.