From: Dive, Aniruddha Mukund (
Date: Mon May 16 2016 - 02:52:14 CDT


I want to track the molecules moving through a specific region of my simulation box and save the trajectory of those molecules in a .gro format. I am currently using a below tcl script for the same.

set distance 5
set nearby [atomselect top "chain G and name C1 O2 and within $distance of name CA"]
set nf [molinfo top get numframes]
set file [open "dump_dol.gro" w]
for {set frame 0} {$frame < $nf} {incr frame 1} {
$nearby frame $frame
$nearby update
puts $file [$nearby get {x y z}]
puts $file "\n"
close $file

But the above script is not working even though the atom selection works perfectly, how do I write the required output trajectory file ?

Kindly help with this issue??


Aniruddha M Dive

PhD student

School of Mechanical and Materials Engg.

Washington State University