#GROMACS Tutorials
Wes Barnett [email protected]
Some GROMACS tutorials for beginners. It's not
necessary to do the tutorials in order, but the first two
tutorials are essential before going on to the others, as the structure file
(methane.pdb) and topology file (topol.top) for methane from tutorial 2 are
used in all subsequent tutorials. The tutorials are designed for GROMACS version
5.1 and up. If you are using an older version, some of the commands or
parameters may have changed. Note especially that the pull code for umbrella
sampling has changed since 5.0 and older releases.
##Prerequisites
I assume you have some working knowledge of the command line. Specifically, you
should know how to make directories, change into them, edit text files, and
download files to your system. When you see a $ or > this is the prompt on
the commandline and indicates you should type the text following it. If the
commandline is new to you, consider going through CodeAcademy's
tutorial.
I also assume you have GROMACS installed on a machine available to you. Source code and installation instructions can be found on the GROMACS documentation page.
Throughout the tutorials we'll be using OPLS methane and TIP4PEW water.
##Contents
- Water - Basics of setting up a simulation. Find out the density of TIP4PEW water.
- One methane in water - How to create a topology file for a molecule and solvate it. Get the radial distribution function.
- Several methanes in water - How to put multiple solutes into a system. Get the methane-methane potential of mean force.
- Free energy of solvation of methane - How to do a free energy simulation when coupling a molecule. Use MBAR to get the result.
- Umbrella sampling - Get methane-methane PMF from umbrella sampling using pull code.
- Test particle insertion - Get the excess chemical potential of methane using test particle insertion.
Some of the other software that I use in these tutorials that you may find useful are: