VMD

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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 CC 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 VMD graphical windows.

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

If getting a blank window on a Mac, try:

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