In molecular dynamics (MD) simulations, a free energy landscape (FEL) serves as a crucial tool for understanding the behavior of molecules and biomolecules over time. It...
In this article, we will generate the topology of a small molecule for AMBER forcefield to be used in MD simulation using GROMACS.
GMXPBSA is a tool to calculate binding free energy [1]. It is compatible with Gromacs version 4.5 and later. In this article, we will install GMXPBSA...
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...
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 have provided a few articles on GROMACS installation on Ubuntu. In this article, we are going to install GROMACS [1] on Mac OS.
It is important to see the behavior of protein during an MD simulation. This can be achieved by taking snapshots in the form of PDB format....
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...
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...
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...
We have provided a tutorial on installing GROMACS [1] on Ubuntu with CUDA GPU support. The methods may vary depending on the requirements of your system....
GROMACS [1] offers a vast range of functions when it comes to molecular dynamics simulation. Today, we are going to explore it for the simulation of...
In this tutorial, we are performing MD simulation in mixed solvents of methanol and water using GROMACS [1,2]. You can follow our previous articles for MD...
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,...
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....
GROMACS [1] is one of the most popular software in bioinformatics for molecular dynamic (MD) studies of macromolecules. We have provided different tutorials regarding MD simulation...
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...
This is a video tutorial of our existing article “Molecular Dynamics (MD) Simulation using GROMACS“.
Molecular dynamics (MD) simulation is an important step in studying the dynamics of macromolecules. In one of the previous articles, MD simulation of chain A of...
This is a video tutorial of our existing article on GROMACS (Abraham, et al. (2015)) installation.
