This is a video tutorial of our existing article on GROMACS (Abraham, et al. (2015)) installation.
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 . 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…)
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  and its result analysis . In this article, we will perform MD simulation for a protein-ligand complex using GROMACS [3, 4]. (more…)
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 . In this article, we will install the nonprofit/academic version of CHARMM on Ubuntu. (more…)