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…
How to generate PSF file for MD simulation using NAMD & VMD?
Protein structure file (PSF) contains topology information and is required for molecular…
Generating topology of molecule for AMBER forcefield for GROMACS.
In this article, we will generate the topology of a small molecule…
How to generate topology from SMILES for MD Simulation?
If you need to generate the topology of molecules using their SMILES,…
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…
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…
Where to find Docking and MD simulation software?
Docking and simulation are two of the methods that are most widely…
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…
Installing GROMOS96 on Ubuntu
GROMOS96 is a well-known software package used for biomolecular simulations . It…
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 of a Protein-Ligand Complex using GROMACS
Previously, we have provided a tutorial on molecular dynamics (MD) simulation of…
Installing CHARMM on Ubuntu
CHARMM (Chemistry at Harvard Molecular Mechanics) is a molecular simulation program that…
