MD Simulation
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
- 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.
MD Simulation
Energy minimization and equilibration of simple protein using NAMD & VMD.

In this tutorial, we will perform energy minimization and equilibration of a simple protein using NAMD [1] & VMD [2]. We are using insulin (PDB ID: 2wfu) for this tutorial.
MD Simulation
Generating topology of molecule for AMBER forcefield for GROMACS.

In this article, we will generate the topology of a small molecule for AMBER forcefield to be used in MD simulation using GROMACS.
MD Simulation
How to visualize output plots of MD simulation (GROMACS)?

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MD Simulation
How to solve ‘Could NOT find CUDA: Found unsuitable version “10.1”‘ error during GROMACS installation?

Compiling GROMACS [1] with GPU can be trivial. Previously, we have provided a few articles on the same. In this article, we will solve an error frequently occurring during GROMACS installation.
MD Simulation
How to calculate number of steps (nsteps) for MD simulation run?

While doing molecular dynamics (MD) simulation, it can be difficult to calculate the number of steps or nsteps for an MD run accurately. In this article, we will learn to calculate nsteps for an MD run. (more…)
MD Simulation
How to install GROMACS on Apple M1 (MacOS)?

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MD Simulation
How to take snapshots of structure at specific times in GROMACS?

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MD Simulation
GROMACS: Uses & Applications

GROMACS stands for GROningen MAchine for Chemical Simulations [1]. It is a very popular and one of the most widely used open-source bioinformatics software. It is generally used for molecular dynamics simulation of macromolecules. In this article, we will explain its uses and applications in bioinformatics studies. (more…)
MD Simulation
Easy installation of GROMACS on Ubuntu 18.04 & 20.04

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…)
MD Simulation
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…)
MD Simulation
How to 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…)
MD Simulation
Tutorial: MD Simulation of small organic molecules using GROMACS

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MD Simulation
Tutorial: MD simulation with mixed solvents using GROMACS

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MD Simulation
Tutorial: MD simulation output analysis of a complex using GROMACS

We have provided several tutorials on molecular dynamics (MD) simulation (please check further reading section). They include installation of simulation software, simulation of a simple protein, and a complex. In this article, we will analyze the GROMACS [1] output of MD simulation of a complex. (more…)
MD Simulation
How to submit MD simulation job on a cluster server using PBS script?

Molecular dynamics (MD) simulation is one of the most widely used methods in bioinformatics. It needs high computation time and therefore, performed on workstations and servers. It requires software to upload and download files to and from the server. In this article, we have explained how to submit MD simulation jobs on cluster computers using PBS scripts. (more…)
MD Simulation
Method-1: Installing GROMACS on Ubuntu with CUDA GPU Support

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MD Simulation
MD Simulation using GROMACS: Things to remember

Molecular dynamics (MD) simulation is considered amongst the important methods in bioinformatics. Installation of MD simulation software and execution of their commands is critical. It requires several parameters to be considered before performing simulations. A single mistake may result in impractical outputs. In this article, we will discuss such important things to remember during the MD simulation and installation and execution of its software (GROMACS) [1,2]. (more…)
MD Simulation
Video Tutorial: MD Simulation using GROMACS

This is a video tutorial of our existing article “Molecular Dynamics (MD) Simulation using GROMACS“.
MD Simulation
Tutorial: MD Simulation of a Protein-Ligand Complex using GROMACS

Previously, we have provided a tutorial on molecular dynamics (MD) simulation of a protein using GROMACS [1] and its result analysis [2]. In this article, we will perform MD simulation for a protein-ligand complex using GROMACS [3, 4]. (more…)
MD Simulation
Installing CHARMM on Ubuntu

CHARMM (Chemistry at Harvard Molecular Mechanics) is a molecular simulation program that can be used for simulation of macromolecules, complexes, and many-particle systems [1]. In this article, we will install the nonprofit/academic version of CHARMM on Ubuntu. (more…)
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