Molecular dynamics
Video tutorial: Installing GROMACS on Ubuntu
This is a video tutorial of our existing article on GROMACS (Abraham, et al. (2015)) installation.
Molecular dynamics
How to generate PSF file for MD simulation using NAMD & VMD?
Protein structure file (PSF) contains topology information and is required for molecular dynamics (MD) simulation in NAMD [1] and VMD [2]. In this tutorial, we will generate a PSF file of a simple protein using NAMD and VMD.
MD Simulation
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 [1]. 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…)
MD Simulation
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 [1] and its result analysis [2]. In this article, we will perform MD simulation for a protein-ligand complex using GROMACS [3, 4]. (more…)
MD Simulation
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 [1]. In this article, we will install the nonprofit/academic version of CHARMM on Ubuntu. (more…)
Molecular dynamics
Tutorial: Molecular dynamics (MD) simulation using Gromacs
Gromacs [1] is one of the most widely used software for molecular dynamics (MD) simulation of macromolecules. One of the previous articles, explains the installation of Gromacs on Ubuntu. This article is about the execution of Gromacs simulating a simple protein. This is a simple tutorial for MD simulation of a protein. (more…)
Algorithms
A new high-level Python interface for MD simulation using GROMACS
The roots of the molecular simulation application can be traced back to physics where it was applied to simplified hard-sphere systems [1]. This field of molecular simulation study has gained a lot of interest since then and applied to perform simulations to fold small protein at multi-microsecond scale [2-4], predict functional properties of receptors and to capture the intermediate transitions of the complex [5], and to study the movement and behavior of ligand in a binding pocket and also to predict interactions between receptors and ligands [6,7]. (more…)
Molecular dynamics
Installing Gromacs on Ubuntu for MD Simulation
In bioinformatics, GROMACS is one of the most popular Molecular Dynamics simulation software with loads of features built-in. Installing GROMACS Version 5.x.x+ can be a tedious and cumbersome process on Ubuntu, especially if you are just starting out. (more…)
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