Connect with us

Molecular dynamics

Video tutorial: Installing GROMACS on Ubuntu

Dr. Muniba Faiza

Published

on

Thumbnail: Video tutorial: Installing GROMACS on Ubuntu

This is a video tutorial of our existing article on GROMACS (Abraham, et al. (2015)) installation.

 

Dr. Muniba is a Bioinformatician based in New Delhi, India. She has completed her PhD in Bioinformatics from South China University of Technology, Guangzhou, China. She has cutting edge knowledge of bioinformatics tools, algorithms, and drug designing. When she is not reading she is found enjoying with the family. Know more about Muniba

Molecular dynamics

How to generate PSF file for MD simulation using NAMD & VMD?

Dr. Muniba Faiza

Published

on

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.

(more…)

Continue Reading

MD Simulation

How to create an index file in GROMACS for MD simulation?

Dr. Muniba Faiza

Published

on

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…)

Continue Reading

MD Simulation

Tutorial: MD Simulation of a Protein-Ligand Complex using GROMACS

Dr. Muniba Faiza

Published

on

md simulation of protein-ligand complex

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…)

Continue Reading

MD Simulation

Installing CHARMM on Ubuntu

Published

on

CHARMM installation 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…)

Continue Reading

Molecular dynamics

Tutorial: Molecular dynamics (MD) simulation using Gromacs

Dr. Muniba Faiza

Published

on

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…)

Continue Reading

Algorithms

A new high-level Python interface for MD simulation using GROMACS

Published

on

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…)

Continue Reading

Molecular dynamics

Installing Gromacs on Ubuntu for MD Simulation

Published

on

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…)

Continue Reading

LATEST ISSUE

ADVERT