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 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.