List of widely used MD Simulation Analysis Tools.
Molecular Dynamics (MD) simulation analysis involves interpreting the vast amounts of data…
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…
![[Tutorial] Installing VIAMD on Ubuntu (Linux).](https://bioinformaticsreview.com/wp-content/uploads/2023/12/viamd.jpg)
[Tutorial] Installing VIAMD on Ubuntu (Linux).
Visual Interactive Analysis of Molecular Dynamics (VIAMD) is a tool that allows…
Energy minimization and equilibration of simple protein using NAMD & VMD.
In this tutorial, we will perform energy minimization and equilibration of a…
Generating topology of molecule for AMBER forcefield for GROMACS.
In this article, we will generate the topology of a small molecule…
How to visualize output plots of MD simulation (GROMACS)?
Visualizing plots of molecular dynamics simulation is easy once you have generated…
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…
How to generate topology of small molecules & ligands for MD Simulation?
Generating the topology of small molecules/ligands is an important step in molecular…
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…
Installing GROMOS96 on Ubuntu
GROMOS96 is a well-known software package used for biomolecular simulations . It…