Contents

VMD installation

VMD 1UBQ

This file:

  • Provides instructions for installing VMD

Keywords: VMD, visualization, atomistic simulations

About VMD:

Humphrey, W., Dalke, A. and Schulten, K., “VMD - Visual Molecular Dynamics”, J. Molec. Graphics, 1996, vol. 14, pp. 33-38.

Associated material:

Installation

Choose the operating system for your VMD installation. In all of the cases, you must download the software from VMD Home page. Select the version that is compatible with your operating system. At this time (Dec. 2020) the latest stable version is 1.9.3. There is also 1.9.4-alpha51. Version 1.9.3 is recommended, but it is also very easy to install both. If you haven’t registered before, you will be asked to register during the process (it’s free).

  • Download from VMD Home Page.

  • Installation using .exe file.

    • Simply install like any other package.

    • Note: 1.9.4-alpha51 is not stable on Windows 10

  • Download from VMD Home Page.

  • Installation is done using a .dmg package.

    • Simply install like any other package.

    • Make sure that you pick the correct package (64 bit for Catalina - the version for Catalina and Big Sur are also different); you can check the version of your MacOS using the Apple logo on the top left corner and then selecting About this Mac.

Unpack:

After downloading (it is assumed that the .tar.gz package was downloaded in the Downloads directory), unpack and move into the new directory:

tar xzf vmd-1.9.3.bin.LINUXAMD64-CUDA8-OptiX4-OSPRay111p1.opengl.tar.gz
cd vmd-1.9.3

Read the README file!

After reading the README file, edit the file called configure if you want to change the default name or the location into which vmd will be installed. Here’s how:

Change name if you want to have multiple versions:

If you want to install different versions of VMD, look for the line that has the variable

install_name = "vmd"

To distinguish between the different versions, you have to give them different names. For example, for vmd-1.9.3 it might be a good idea to do the following:

install_name = "vmd-1.9.3"

and for vmd-1.9.4-alpha51

install_name = "vmd-1.9.4-a51"

where the part a51 is to indicate the particular alpha version that was available at the time; it is useful to have the version name in case one wants to install another version later.

Install & library directories:

The default install and library directories are given by the variables install_bin_dir and install_library_dir. The defaults are:

install_bin_dir="/usr/local/bin"
install_library_dir="/usr/local/lib/$install_name

If you have root privileges and want to install VMD system-wide, then nothing needs to be done. If you don’t have root rights or/and want to have a private installation, change the above to whatever you want.

Configure:

Run ./configure to generate a Makefile:

./configure

The output looks something like

sam@linux:~/Downloads/vmd-1.9.3$ ./configure 
using configure.options: LINUXAMD64 OPENGL OPENGLPBUFFER FLTK TK ACTC CUDA IMD LIBSBALL XINERAMA XINPUT LIBOPTIX LIBOSPRAY LIBTACHYON VRPN NETCDF COLVARS TCL PYTHON PTHREADS NUMPY SILENT ICC

Final step: The actual installation:

The above puts the new Makefile in the directory ./src. Move there

cd src

Pick one of the installation commands below depending on if you want a system-wide installation or if you modified the installation and library directories to local ones that do not require root access:

For system-wide installation:

sudo make install

For private installation (requires that installation and library directories were changed as discussed above):

sudo make install

The output looks something like

sam@linux:~/Downloads/vmd-1.9.3/src$ sudo make install
[sudo] password for sam: 
Info: /bin/csh shell not found, installing Bourne shell startup script instead
Make sure /usr/local/bin/vmd is in your path.
VMD installation complete.  Enjoy!

If you changed the name as above, start vmd from the command line using

vmd-1.9.3

and otherwise using

vmd
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