VMD-L Mailing List

From: ban arn (ban.arn_at_gmail.com)
Date: Wed Nov 02 2011 - 14:41:09 CDT

Dear VMD users

I would like to calculate radius of gyration for trajectory and i'm using
script like this

set mol [molinfo top]
set out [open test04.txt w]
 set sel [atomselect top "resid 101 93 80 49 39"]
 set frames [molinfo $mol get numframes]
 for {set i 0} {$i < $frames} {incr i} {
   $sel frame $i
   $sel update
   lappend a [measure rgyr $sel]
   puts $out "$i $a"
}
$sel delete

It produces huge ouput and i'm puzzling whether i'm doing calculating
correctly or not.

I expect one value for each trajectory & i'm getting output as like matrix.

Kindly advice.

Many Thanks
Balaji