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Installing GROMOS96 on Ubuntu

Dr. Muniba Faiza

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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.

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

  1. 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 A103(19), 3596-3607.

Dr. Muniba is a Bioinformatician based in New Delhi, India. She has completed her PhD in Bioinformatics from South China University of Technology, Guangzhou, China. She has cutting edge knowledge of bioinformatics tools, algorithms, and drug designing. When she is not reading she is found enjoying with the family. Know more about Muniba

MD Simulation

Easy installation of GROMACS on Ubuntu 18.04 & 20.04

Dr. Muniba Faiza

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Installing GROMACS on ubuntu

We have provided several articles on GROMACS [1] installation on Ubuntu including the easy installation method for GROMACS version 5.x.x. In this article, we will provide shell scripts to install the latest (2021 series) of GROMACS on Ubuntu 18.04 and 20.04. (more…)

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MD Simulation

How to create an index file in GROMACS for MD simulation?

Dr. Muniba Faiza

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How to create an index file in GROMACS for MD simulation?

MD simulation is a tricky technique if you don’t understand what you are doing through various parameters and algorithms in GROMACS [1]. That may lead to several errors. In this article, we are going to create an index file for the protein groups in GROMACS to solve such errors. (more…)

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MD Simulation

How to generate topology of small molecules & ligands for MD Simulation?

Dr. Muniba Faiza

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generate topology of small molecules & ligands for MD simulation

Generating the topology of small molecules/ligands is an important step in molecular dynamics (MD) Simulation. We explained it in previous articles as part of MD simulation tutorials. In this article, we will explain how can you generate the topology of ligands for MD simulation of complex or small molecules only. (more…)

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