VMD-L Mailing List

From: maria goranovic (mariagoranovic_at_gmail.com)
Date: Fri Jul 08 2011 - 09:56:14 CDT

Hi Axel

Thank you for the help. However, I am not much of an expert in tcl or vmd
scripting and am learning. Hopefully I can please get some help?

One difference between your setup and mine seems to be that in your setup
all the data over frames which you are trying to import is lying in one
file, and you read the file one at a time?

So, here: each line is being read from zundel.dip and assigned to the
dipdata($i) array.

for {set i 0} {$i < $n} {incr i} {
# advance selection to the current frame and update.
$sel frame $n
$sel update
set dipdata($i) [list [center_of_mass $sel] [gets $dip]]
}
close $dip

However, the data I need to read in each frame is not one line, but an
entire file.

Secondly, I did not really understand what seems to be the key command:

trace variable vmd_frame(0) w do_dipdraw

This means that the command do_dipdraw will be executed if vmd_frame(0) is
executed? what is the w for? what is vmd_frame(0) ?

Thank you again,

Maria

On Fri, Jul 8, 2011 at 3:31 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> On Fri, Jul 8, 2011 at 8:59 AM, maria goranovic
> <mariagoranovic_at_gmail.com> wrote:
> > Hi
> > I have a trajectory, and I want to source in a different draw-command
> > containing file on each frame. The files to be sourced in contain several
> > draw commands as below:
> > ...
> > draw point { 67.340 84.391 32.398}
> > draw point { 67.340 84.391 32.340}
> > draw point { 67.340 84.410 32.284}
> > draw point { 67.340 84.446 32.238}
> > draw point { 67.340 84.495 32.206}
> > draw point { 67.340 84.552 32.192}
> > draw point { 67.340 84.611 32.196}
> > draw point { 67.340 84.664 32.220}
> > draw point { 67.340 84.707 32.260}
> > draw point { 67.340 84.735 32.311}
> > draw point { 67.353 84.567 32.605}
> > ...
> >
> > the idea is to view the trajectory and draw a new set of points each
> frame.
> > Can someone please suggest how to accomplish this?
> > I tried something like the following to load 5 frames from a 125-frame
> > trajectory. The files temp_$j.vmd_plot contain data like the above. The
> > script below works, except that only the last set of points i.e.
> > outputhole_5.vmd_plot are displayed, and no others. When I look back into
> > the trajectory, VMD has lost information of previous temp_$j.vmd_plot
> files.
> > How do I keep the data in the display?
>
> that is not how this will work.
>
> have a look at item 5.2 in this document.
>
>
> http://sites.google.com/site/akohlmey/redirect/cpmd-vmd.pdf?attredirects=0&d=1
>
> cheers,
> axel.
>
>
> > ====================
> > mol load gro protein-aligned-50ns.gro
> > # Load trajectory
> > for {set j 0} {$j < 5 } {incr j} {
> > # i goes like 1, 26, 51 ...
> > set i [expr ($j*25)+1]
> > # k goes like 25, 50, 75 ...
> > set k [expr ($j+1)*25]
> > mol addfile {protein-aligned.xtc} type {xtc} first $i last $k step 25
> > waitfor 1 0
> > # this file contains the draw statements
> > source temp_$j.vmd_plot
> > }
> > ========================
> >
> > --
> > Maria G.
> > Technical University of Denmark
> > Copenhagen
> >
>
>
>
> --
> Dr. Axel Kohlmeyer
> akohlmey_at_gmail.com http://goo.gl/1wk0
>
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA.
> 

-- 
Maria G.
Technical University of Denmark
Copenhagen