[[ https://www.ks.uiuc.edu/Research/vmd/ | VMD Home ]]

====== Installation ======
  * download package and extract to a tmp dir.
  * edit configure:
<code>
$install_bin_dir=/home/usr/bin
$install_library_dir=/home/usr/share/$install_name
</code>
  * run the following commands
<code>
./configure
cd src
make install
</code>

  * Install plug-ins including catdcd (VMD 1.9 already shipped with plug-ins)
    * download plug-ins from http://www.ks.uiuc.edu/Research/vmd/plugins/ (normally at the bottom of the page, e.g. Plugin updates: VMD 1.8.6 compatible plugins for all platforms)
    * Copy the new files under the correct platform folder to /home/usr/share/vmd/plugins. (For VMD-1.8.7, I only copied bin folder in VMD-1.8.6-compatible plugins)

====== Resources ======
  * [[http://www.ks.uiuc.edu/Research/vmd/vmd_help.html | VMD quick help]]
====== Tcl script ======
===== Run a script =====
  * You can run tcl script in VMD console or VMD TCL console by "source ***.tcl". However, it does not output the content of puts command. (strange)
<code>
source myscript.tcl
</code>
  * To run a script out side of VMD GUI interface (Note: vmd state file is also tcl script!)
<code>
vmd -dispdev text -e myscript.tcl
</code>

===== Startup script =====
  * On startup, VMD searches .vmdrc in the following paths: '.', '%%$HOME%%', '%%$VMDDIR%%'. ONLY the first file found will be executed.
  * What I did is to copy %%$VMDDIR%% to %%$HOME%%, and add one line at the end of the file (to load some useful functions).
<code>
...
source /home/yxue/codelib/tcl/vmd.tcl
</code>

===== Access plugin in text mode =====
  * Run the following (take saltbr as an example)
<code>
vmd -dispdev text
# Now we are in the text console
package require saltbr
# Now saltbr command is available
</code>
====== Make Movie ======
===== Windows =====
Note: videomach is required. It is a shareware. You can download it here [{{.:videomach.rar].}} An unlimited version is also included just for testing :-)
  * Suppose we are going to generate a movie for denatured drkN-SH3. We have a bunch of dcd files in D:\nathan_drk
  * Load psf file in VMD first.
  * If there are only a couple of dcd files, manually loading dcd files is ok. However, we have 100 dcd files here, so the better solution is to use a loop in VMD console to load them. Considering the limited memory, let's load them 10 by 10. The tcl code is posted here. You'd better to save it as, say, loadtraj.tcl under C:/Documents and Settings/yxue, and run it in VMD console by "source loadtraj.tcl".
<code>
set dir d:/nathan_drk
set n 1

for {set i [expr ($n-1)*10+1]} {$i <= [expr $n*10]} {incr i} {
  set fndcd $dir/traj_$i.dcd
  mol addfile $fndcd waitfor all
}
</code>
  * turn off coordinate icon by menu: display->Axes->off
  * Adjust windows size of "VMD display" which decides the display size of video
  * choose menu "Extensions"/"Visualization"/"Movie Maker"
  * In "VMD movie generator" dialog, choose "movie settings"->trajectory
  * click "make movie"

===== Linux =====
  * other options: mjpegtools, mencoder; http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/11441.html
  * mpegtools: http://mjpeg.sourceforge.net/
  * mpegtools tutorial: http://mjpeg.sourceforge.net/files/mjpeg-howto.pdf

====== Make gif animation ======
  * ref: http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/animated_gif/