From: ban arn (ban.arn_at_gmail.com)
Date: Wed Nov 02 2011 - 16:02:45 CDT

Thanks Axel

Balaji

On Wed, Nov 2, 2011 at 8:49 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

>
>
> On Wed, Nov 2, 2011 at 3:41 PM, 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.
>>
>
> that is because of the lappend. you don't need it.
> just use:
>
> puts $out "$i [measure rgyr $sel]"
>
> the $sel update is also not needed with your selection.
> $sel update is only required, if the selected atoms would
> change from frame to frame, e.g. from using "within"
> keyword or a selection by coordinate. that should make
> the script much faster.
>
> cheers,
> axel.
>
>
>
>
>> Kindly advice.
>>
>> Many Thanks
>> Balaji
>>
>>
>
>
> --
> Dr. Axel Kohlmeyer
> akohlmey_at_gmail.com http://goo.gl/1wk0
>
> College of Science and Technology
> Temple University, Philadelphia PA, USA.
>