GROMACS Crash Course

GROMACS is a very potent and versatile Open Source Molecular Dynamics simulation program. Since it has no GUI, one has to start, control and run it via the terminal or a shell script.

During the following two days you will

1. learn how to use the Unix/Linux shell (via a terminal),
2. install GROMACS,
3. learn basic GROMACS usage.

During the course it will be assumed that you have Ubuntu 18.04 installed on your Notebook. Further, you will need internet access.

1. The Unix Shell

To install and use GROMACS a basic knowledge regarding the use of the Unix/Linux shell is mandatory. Thus, you will start with a "Software Carpentry" Unix shell lesson via the following link:

http://swcarpentry.github.io/shell-novice/ .

Before doing so, please update your system via

sudo apt-get update && sudo apt-get upgrade

and install my favorite text editor emacs via

sudo apt-get install emacs.

You can find a "cheat sheet" (aka reference card) concerning Emacs usage here

https://www.gnu.org/software/emacs/refcards/pdf/refcard.pdf .

Shell Variables

After finshing the Unix shell lesson you might want to take a look on Shell Variables

https://carpentries-incubator.github.io/shell-extras/08-environment-variables/index.html ,

since the usage of GROMACS requires some basic knowledge of these and even has its own variables.

2. Install GROMACS

You will install GROMACS 2018 (for documentation see: http://manual.gromacs.org/documentation/2018.8/index.html). Before doing so, you should update our system via

sudo apt-get update && sudo apt-get upgrade.

Afterwards, at first, you have to download the GROMACS source code from

http://manual.gromacs.org/documentation/2018.8/download.html#source-code

and perform the installation following the instructions on

http://manual.gromacs.org/documentation/2018.8/install-guide/index.html .

You should try the "quick and dirty" installation first, but if you run into trouble in doing so, you might need to try the more elaborated instructions. Please read on before actually performing the installation procedure.

GROMACS is installed in the directory to which CMAKE_INSTALL_PREFIX points. It may not be the source directory or the build directory. Performing the "quick-and-dirty" installation under Ubuntu it will point to /usr/local/gromacs by default. You require write permissions to this directory. Thus, without super-user privileges, CMAKE_INSTALL_PREFIX will have to be within your home directory. Even if you do have super-user privileges, you should use them only for the installation phase, and never for configuring, building, or running GROMACS!

If, during the build process with CMake, while executing

cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON,

you run into an error like

  No CMAKE_CXX_COMPILER could be found.

  Tell CMake where to find the compiler by setting either the environment
  variable "CXX" or the CMake cache entry CMAKE_CXX_COMPILER to the full path
  to the compiler, or to the compiler name if it is in the PATH.


-- Configuring incomplete, errors occurred!

you are missing the C++ compiler. This can be solved by installing essential compilers and related packages via

sudo apt-get install build-essential

Also, if you want to get the most out of our hardware, i.e., when using a supercomputer, it will be necessary to perform a optimized installation, taking into account specific features of the respective hardware and OS.

How to get access to GROMACS after the installation

GROMACS installs the script GMXRC in the bin subdirectory of the installation directory (e.g. /usr/local/gromacs/bin/GMXRC), which you can source from your shell to tell the system were to find the GROMACS executables:

source /your/installation/prefix/here/bin/GMXRC.

It will detect what kind of shell you are running and set up your environment for using GROMACS. You should arrange for your login scripts to do this automatically:

1. Go to your home directory via bash cd ~,
2. Open the file .bashrc with an editor, e.g., with emacs via emacs .bashrc,
3. Add source /your/installation/prefix/here/bin/GMXRC to the end of the file and save it (e.g., via "Ctrl"+"X"+"S"),
4. Open a new terminal to activate the changes (i.e., source GMXRC). Now test, if you can easily execute GROMACS via executing gmx -version.

3. Using GROMACS

Diving into GROMACS for the first time, it is sensible to start with a very basic and well-tried tutorial like

http://www.mdtutorials.com/gmx/lysozyme/index.html

were you will set up a simulation system containing a protein (lysozyme) in a box of water and with ions.

After mastering this, you will go ahead with a more complex and use-case specific tutorial

http://www.mdtutorials.com/gmx/complex/index.html

were you will set up a simulation system containing a protein (T4 lysozyme L99A/M102Q) in complex with a ligand.

In doing so, you have learend the basic concepts and some more advanced aspects of working with GROMACS (more precisely: of setting up simulation systems with GROMACS).

4. Simulating on a supercomputer

Performing MD simulations on a normal laptop or desktop PC isn't going to be very productive, since the computing ressources of such a small consumer systems aren't very grand and MD simulations of large biomolecular systems are computationally very costly. Thus, real large-scale production simulations are typically performed on a cluster or supercomputer enabling the execution of highly parallel calculations on hunreds or thousands of CPUs or even potent GPUs.

To do so, the first thing you need is access to such a supercomputer, i.e. the Lichtenberg Supercomputer (HHLR) of the TU Darmstadt.

Secondly, you need a way to actually access the remote computer, since you won't drive to Darmstadt and log into the supercomputer locally. A simple and common (often even the only) way to do so is via ssh (secure shell). Following the link

https://carpentries-incubator.github.io/shell-extras/02-ssh/index.html

you will see how to use ssh and also scp (secure copy).