VMD-L Mailing List

From: Dive, Aniruddha Mukund (aniruddha.dive_at_wsu.edu)
Date: Mon May 16 2016 - 12:57:18 CDT

Hi Chitrak,

When I load the tcl file it does nothing, does not give me any errors nor does it run and creates an output file. The tcl window remains blank.

Regards,

Aniruddha M Dive

PhD student

School of Mechanical and Materials Engg.

Washington State University

________________________________
From: Chitrak Gupta <chgupta_at_mix.wvu.edu>
Sent: Monday, May 16, 2016 9:30 AM
To: Dive, Aniruddha Mukund
Cc: vmd-l_at_ks.uiuc.edu
Subject: Re: vmd-l: TCL script to track molecules moving within a specified region each time frame

Hi Aniruddha,

When you say "the script is not working", what does it do? Does it give an error? If not, what is it?
?

Best,
Chitrak.

On Mon, May 16, 2016 at 3:52 AM, Dive, Aniruddha Mukund <aniruddha.dive_at_wsu.edu<mailto:aniruddha.dive_at_wsu.edu>> wrote:

Hi,

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??

Thanks,

Aniruddha M Dive

PhD student

School of Mechanical and Materials Engg.

Washington State University