VMD

Using pre-installed VMD

Connect with ssh -X/-Y or via VNC to have graphics enabled.

There are, currently, two versions of VMD available on our clusters:

$ module avail vmd
...
------------------ Compiler-dependent avx2 modules ----------------------
   vmd/1.9.3 (L,vis)    vmd/1.9.4a43 (vis,D)

The default version is 1.9.4a43. To use it:

[name@server ~]$ module load vmd
[name@server ~]$ vmd

This should open VMD graphical windows.

You can also specify the version if you want to use the older one:

$ module load vmd/1.9.3

Instructions for installing version 1.9.4 Alpha

1. Download the 1.9.4 LATEST ALPHA tar file from 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 with:

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

4. Enter the created directory by:

cd vmd-1.9.4*

5.

mkdir ~/vmd_install
mkdir ~/vmd_library

6. edit the configure file to read

# 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";

but replace your_user_name with your actual user name.

7. Run configure:

./configure

8. Run make

cd src
make install

9. Add the resulting executable to your path

export PATH=~/vmd_install:$PATH

Also, modify the RPATH of vmd files so it does not use libraries in /usr on our system

cd
cd vmd_library/
setrpaths.sh  --path .

If getting a blank window on a Mac, try:

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

Installing plugins

VMD has many plugins available. You should be able to install them in your own space. The example that follows will illustrate how to install the CaFE plugin.

The installation instructions are detailed 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

Then edit the .vmdrc file with

nano .vmdrc

and add this line:

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

After this load the vmd module and the other modules (namd) which are required, and the CaFE plugin should be available.

Links

• WestGrid webinars
  • Molecular visualization with VMD
  • Intermediate VMD topics - Trajectories, movies, scripting