Install GROMOS Molecular Dynamics software under Linux (Ubuntu) to setup protein simulations and convert topologies to GROMACS format

Combine GROMOS and GROMACS Software packages

© Erik Breslmayr, 2021

GROMOS is a software package to setup and run Molecular Dynamics Simulations. Gromos is more known for its force fields, than for running simulations with it. Therefore, this guide should help you to install GROMOS and use it to setup your simulation with Gromos force fields. The generated topologies can be easily transformed into Gromacs topologies and the simulation can also be setup and started by using GROMACS.

Tested under Ubuntu_20.04 LTS

Download GROMOS

• Create an account and after logging in you can download the latest release of the Gromos packages.

Gromos++ package includes all tools to setup a simulation and to analyse it

Gromos MD++ package includes the MD engine, which can be compiled using CUDA for running the solvent on Nvidia graphic cards, which increases the simulation speed

Gromos force field package includes the newest force field developed (protein, sugars, cofactors)

Download and install additonal libraries

• GNU Scientific Library
• Download and Extract the archieve (e.g. tar -xvf gsl-latest.tar.gz)
• Within the folder (e.g. gsl-2.6) install gsl

./configure

make

sudo make install

• FFTW library
• Download and Extract the archieve (e.g. tar -xvf fftw-3.3.9.tar.gz)
• Within the folder (e.g. gsl-2.6) install gsl

./configure

make

sudo make install

Install Gromos++

• Extract gromos++ archieve (e.g. tar -xvf gromos++.tar.gz)
• Within the folder (e.g. gromos++-1.5.0) make a build folder (mkdir build)
• Go to the build folder and compile gromos++

./../configure --with-gsl=/usr/local --with-fftw=/usr/local

make

sudo make install

• The binaries are located within the bin folder (e.g. make_top)
• To make all tools available, the bin folder has to be in the local Path to make them executable.
• Copy the gromos++ folder to a location you want to store it (e.g. ~/programs) and add the Path variable to the .bashrc file
• export PATH=~/programs/gromos++-1.5.0/build/bin:$PATH
• Finally source the .bashrc file source .bashrc

To enable addidional tools such as OutGromacs, which transforms Gromos topologies into Gromacs topologies you have to make OutGromacs in the src/gio folder within your gromos++ build folder.

make OutGromacs

You can link the OutGromacs tool to the bin folder to make it executable. Therefore, go to the bin folder within your build and link it.

ln -s ../src/gio/OutGromacs

Install Gromos MD++

• Do the same as for Gromos++ installation (md++ folder).
• To make all tools available, the bin folder has to be in the local Path to make them executable.
• Copy the md++ folder to a location you want to store it (e.g. ~/programs) and add the Path variable to the .bashrc file
• export PATH=~/programs/md++-1.5.0/build/bin:$PATH
• You also have to add the gsl libraries to the lib path for the md engine
• export LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH
• Finally source the .bashrc file source .bashrc