Installing GROMOS96 on Ubuntu

GROMOS96 is a well-known software package used for biomolecular simulations [1]. It can be used for the molecular dynamics simulation of protein, peptide, and protein-ligand complex as well. In this article, we will install GROMOS96 on Ubuntu.

Contents

Getting started Downloading GROMOS96 Installing pre-requisites Installing GNU Scientific Library Installing FFTW3 Installing GROMOS96 Installing md++ package Installing forcefields Installing GROMOS96 References

Getting started

Let’s update and upgrade the system first.

$ sudo apt-get update

$ sudo apt-get upgrade

Downloading GROMOS96

You will have to register yourself for downloading the software package. Click here to register/login. After successful registration, you will see a list of files including tutorials in PDF format. Download all files but in this tutorial, we will be using the following three files:

GROMOS Force-Field Files
GROMOS MD++ simulation software
GROMOS Tutorial Files

Installing pre-requisites

GROMOS requires the following two libraries to be installed on your system. If already installed then skip to the next step.

GNU Scientific Library
FFTW3

Installing GNU Scientific Library

$ sudo apt-get install libgsl0 libgsl0-dev

Installing FFTW3

$ sudo apt-get install libfftw3-3 libfftw3-dev

Installing GROMOS96

We will first install the md++ package, followed by forcefields and gromos++.

Installing md++ package

Change to the directory where you have downloaded the package. Let’s say Downloads. Open a terminal by pressing Ctrl+Alt+T and type the following commands:

$ cd Downloads/

$ tar xvzf md++.tar.gz

$ cd md++-1.4.1/

Make a directory namely, ‘ARCHITECTURE’ and change to it.

$ mkdir ARCHITECTURE

$ cd ARCHITECTURE/

$ ../configure

$ make

$ sudo make install

$ mkake clean

Installing forcefields

$ tar xvzf forcefields.tar.gz

Installing GROMOS96

$ xvzf gromos++.tar.gz

$ cd gromos++-1.4.1/

$ ./configure

$ make

$ make check

$ sudo make install

$ make clean

Add gromos++ to your path. Open the bashrc file and add the following commands at the end of the file.

$ sudo gedit ~/.bashrc

$ export PATH="${PATH}:/home/user/Downloads/gromos++/bin"

$ export LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:/home/user/Downloads/gromos++/lib"

Don’t forget to replace user with your username.

References

Scott, W. R., Hünenberger, P. H., Tironi, I. G., Mark, A. E., Billeter, S. R., Fennen, J., … & van Gunsteren, W. F. (1999). The GROMOS biomolecular simulation program package. The Journal of Physical Chemistry A, 103(19), 3596-3607.