From: Grace Brannigan (grace.brannigan_at_rutgers.edu)
Date: Fri Jul 05 2013 - 14:26:47 CDT

Alternatively (or perhaps additionally) a new selection (ref) is made every
frame without deleting it after usage, so you could be running out of
memory. Rather than making the new selection each time you could try just
including the line

$ref frame $frame

within the loop.

cheers,
Grace

On Fri, Jul 5, 2013 at 1:17 PM, Jérôme Hénin <jerome.henin_at_ibpc.fr> wrote:

> Hi,
>
> This could just be incomplete file I/O. Add a line saying "close $outfile"
> at the end to flush the buffer.
>
> Cheers,
> Jerome
>
>
> ----- Original Message -----
> > Hi,
> >
> > I am trying to make a script that will display the center of mass of
> > a
> > chosen residue in my simulation. I have run into some issues with the
> > tcl where I am not familiar with the syntax.
> >
> > My first issues is that I would like to loop over all the frame in my
> > simulation
> >
> > set numframes [molinfo 0 get numframes]
> > # Returns 1124 frames which is correct
> > # Loop over frames
> >
> > for {set frame 0} {${frame} < ${numframes}} {incr frame} {
> >
> > set ref [atomselect 0 "resname CFN" frame ${frame}]
> > set com_ref [measure center ${ref} weight mass]
> > puts $outfile "Frame $frame com $com_ref"
> >
> > draw sphere $com_ref radius 0.5
> >
> > }
> >
> > My problem is that it only outputs 1104 frames and not 1124 as I
> > would
> > expect it to do?
> >
> > Thanks
> >
>

-- 
Grace Brannigan, Ph.D.
Assistant Professor
Center for Computational and Integrative Biology (CCIB) &
Department of Physics
Rutgers University, Camden, NJ
(856)225-6780
www.branniganlab.org