<languages />
[[Category:Software]][[Category:BiomolecularSimulation]]


"VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting."
The VMD web site is [https://www.ks.uiuc.edu/Research/vmd/ here].

== Using a pre-installed version ==

Connect to a cluster using [[VNC]], <code>ssh -X</code>, or <code>ssh -Y</code>, in order to enable graphics.  
We recommend using VNC for best performance.

To run the default version of VMD, currently <code>1.9.4a43</code>, do:
{{Commands
|module load vmd
|vmd
}}
This should open VMD graphical windows.

See [[Using modules]] for more on the <code>module</code> command, including how to find and use other pre-installed versions.

== Installing version 1.9.4 Alpha ==

1. Download the 1.9.4 LATEST ALPHA tar file from [http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD http://www.ks.uiuc.edu/], selecting the LINUX_64 version.  Free registration is required.

2. Copy the file to the home directory of the cluster you wish to use.

3. Unpack the file:

 tar xvf vmd-1.9.4*.opengl.tar.gz

4. Enter the newly-created directory:

 cd vmd-1.9.4*

5. Create two new directories to receive the program files:

 mkdir ~/vmd_install
 mkdir ~/vmd_library

5. Edit the <code>configure</code> file to read as follows, replacing each instance of <code>your_user_name</code> with your actual user name:

 # Directory where VMD startup script is installed, should be in users' paths.
 $install_bin_dir="/home/your_user_name/vmd_install";
 
 # Directory where VMD files and executables are installed
 $install_library_dir="/home/your_user_name/vmd_library";

6. Run <code>configure</code> and <code>make</code>:

 ./configure
 cd src
 make install

7. Add the resulting executable to your path:
 export PATH=~/vmd_install:$PATH

8. Use <code>setrpaths.sh</code> to modify the VMD executables so they use libraries from CVMFS:
 cd ~/vmd_library/
 setrpaths.sh  --path .

If you are using a Mac and getting a blank window, try running this:

 defaults write org.macosforge.xquartz.X11 enable_iglx -bool true

== Installing plugins ==

VMD has many plugins available.  You can install them in your own space.  
The example that follows illustrates how to install the [https://github.com/HuiLiuCode/CaFE_Plugin CaFE plugin],
from detailed instructions which can be found [https://github.com/HuiLiuCode/CaFE_Plugin/blob/master/doc/manual.pdf here]:

 wget https://github.com/HuiLiuCode/CaFE_Plugin/archive/refs/heads/master.zip
 unzip master.zip
 cd CaFE_Plugin-master
 mv src cafe1.0
 mv cafe1.0 ~
 cd

Edit the <code>.vmdrc</code> file with your favorite editor (<code>nano, vim, emacs</code> etc.) and add this line:

 set auto_path [linsert $auto_path 0 {~/cafe1.0}]

After this, load the <code>vmd</code> module and any other modules which are required, such as <code>namd</code> and the CaFE plugin should be available.

== Links ==

* WestGrid webinars (in English)
** [https://www.youtube.com/watch?v=_skmrS6X4Ys Molecular visualization with VMD] 
** [https://www.youtube.com/watch?v=Jce5JN2fLuo Advanced VMD: Trajectories, movies, scripting]