VMD

"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 here.

Using a pre-installed version

Connect to a cluster using VNC, ssh -X, or ssh -Y, in order to enable graphics. We recommend using VNC for best performance.

The run the default version of VMD, currently 1.9.4a43, do:

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

This should open VMD graphical windows.

See Using modules for more on the module command, including how to find and use other pre-installed versions.

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:

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 configure file to read as follows, replacing each instance of your_user_name 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 configure and make:

./configure
cd src
make install

7. Add the resulting executable to your path:

export PATH=~/vmd_install:$PATH

8. Use setrpaths.sh 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 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

CernVM File System