Free_Energy_Landscape-MD: Python package to create Free Energy Landscape using PCA from GROMACS.
In molecular dynamics (MD) simulations, a free energy landscape (FEL) serves as…
Generating topology of molecule for AMBER forcefield for GROMACS.
In this article, we will generate the topology of a small molecule…
How to install GMXPBSA on Ubuntu (Linux)?
GMXPBSA is a tool to calculate binding free energy . It is…
How to solve ‘Could NOT find CUDA: Found unsuitable version “10.1”‘ error during GROMACS installation?
Compiling GROMACS with GPU can be trivial. Previously, we have provided a…
How to calculate number of steps (nsteps) for MD simulation run?
While doing molecular dynamics (MD) simulation, it can be difficult to calculate…
How to install GROMACS on Apple M1 (MacOS)?
We have provided a few articles on GROMACS installation on Ubuntu. In…
How to take snapshots of structure at specific times in GROMACS?
It is important to see the behavior of protein during an MD…
GROMACS: Uses & Applications
GROMACS stands for GROningen MAchine for Chemical Simulations . It is a…
Easy installation of GROMACS on Ubuntu 18.04 & 20.04
We have provided several articles on GROMACS installation on Ubuntu including the…
How to create an index file in GROMACS for MD simulation?
MD simulation is a tricky technique if you don't understand what you…
Method-2: Installing GROMACS on Ubuntu 20.04 with CUDA GPU Support
We have provided a tutorial on installing GROMACS on Ubuntu with CUDA…
Tutorial: MD Simulation of small organic molecules using GROMACS
GROMACS offers a vast range of functions when it comes to molecular…
Tutorial: MD simulation with mixed solvents using GROMACS
In this tutorial, we are performing MD simulation in mixed solvents of…
Tutorial: MD simulation output analysis of a complex using GROMACS
We have provided several tutorials on molecular dynamics (MD) simulation (please check…
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…
Method-1: Installing GROMACS on Ubuntu with CUDA GPU Support
GROMACS is one of the most popular software in bioinformatics for molecular…
MD Simulation using GROMACS: Things to remember
Molecular dynamics (MD) simulation is considered amongst the important methods in bioinformatics.…
Video Tutorial: MD Simulation using GROMACS
This is a video tutorial of our existing article "Molecular Dynamics (MD)…
Tutorial: MD simulation output analysis of protein using GROMACS
Molecular dynamics (MD) simulation is an important step in studying the dynamics…
Video tutorial: Installing GROMACS on Ubuntu
This is a video tutorial of our existing article on GROMACS (Abraham,…