VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Jul 08 2011 - 08:31:17 CDT

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.