In this article, we are going to install VMD [1] on Ubuntu.

Preparing system

Update and upgrade your system before installing VMD. Open a terminal by pressing Ctrl+Alt+T and paste the following commands.

$ sudo apt-get update

$ sudo apt-get upgrade

Downloading VMD

Go to this page and select an appropriate VMD version compatible with your system. To download VMD, you will have to register using your university email address. After successful registration, it will automatically start downloading. Here, we are downloading VMD 1.9.3, not the latest alpha version as it is a test version, therefore, you might face some issues.

Installing VMD

Go to the directory where you have downloaded the tar file and extract. Let’s say we have downloaded this file in the Downloads directory.

$ cd Downloads/

$ tar xvzf vmd-1.9.3.bin.LINUXAMD64-CUDA102-OptiX650-OSPRay185.opengl.tar.gz

It will create a new directory, namely, vmd-1.9.3.

Move inside this new directory and install as shown below.

$ cd vmd-1.9.3/

Now, open the file configure and change the $install_bin_dir and $install_library_dir if you wish otherwise leave the default values as it is. Now paste the following command.

$ ./configure

Now, move inside the src directory to install.

$ cd src/

$ sudo make install

It will take a moment to finish the installation. Now, you can type vmd in the terminal and it should work. However, sometimes, it does not work that way. You have to add it to the path. For that, follow the steps given below.

$ sudo nano ~/.bashrc

Go to the end of the file and paste the following:

$ /path/to/vmd

For example, $ /usr/local/bin/vmd

Save and exit.

$ source ~/.bashrc

If it still doesn’t open then add the following path instead of the above.

$ /usr/local/bin/vmd/vmd_LINUXAMD64

$ source ~/.bashrc

Now, it should work properly.

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References

1. Humphrey, W., Dalke, A., & Schulten, K. (1996). VMD: visual molecular dynamics. Journal of molecular graphics, 14(1), 33-38.