[[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]], ssh -X, or ssh -Y, in order to enable graphics. We recommend using VNC for best performance. To run the default version of VMD, currently 1.9.4a43, do: {{Commands |module load vmd |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. == 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 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 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 .vmdrc file with your favorite editor (nano, vim, emacs etc.) and add this line: set auto_path [linsert $auto_path 0 {~/cafe1.0}] After this, load the vmd module and any other modules which are required, such as namd 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]