VMD-L Mailing List

From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Wed Nov 02 2011 - 16:14:59 CDT

Hi,

Try "set a [measure rgyr $sel]". With lappend you are adding the
gyration radius for each frame to a list and then outputting the whole list.

Regards,
Ajasja

On Wed, Nov 2, 2011 at 20:41, ban arn <ban.arn_at_gmail.com> wrote:

> 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
>
>