In molecular dynamics (MD) simulations, a free energy landscape (FEL) serves as a crucial tool for understanding the behavior of molecules and biomolecules over time. It...
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...
In this article, we will generate the topology of a small molecule for AMBER forcefield to be used in MD simulation using GROMACS.
If you need to generate the topology of molecules using their SMILES, a simple Python script is available.
Compiling GROMACS [1] with GPU can be trivial. Previously, we have provided a few articles on the same. In this article, we will solve an error...
While doing molecular dynamics (MD) simulation, it can be difficult to calculate the number of steps or nsteps for an MD run accurately. In this article,...
GROMACS stands for GROningen MAchine for Chemical Simulations [1]. It is a very popular and one of the most widely used open-source bioinformatics software. It is...
We have provided several articles on GROMACS [1] installation on Ubuntu including the easy installation method for GROMACS version 5.x.x. In this article, we will provide...
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...
Docking and simulation are two of the methods that are most widely used in bioinformatics. In this article, we provide all important links to the software...
Generating the topology of small molecules/ligands is an important step in molecular dynamics (MD) Simulation. We explained it in previous articles as part of MD simulation...
GROMACS [1] offers a vast range of functions when it comes to molecular dynamics simulation. Today, we are going to explore it for the simulation of...
In this tutorial, we are performing MD simulation in mixed solvents of methanol and water using GROMACS [1,2]. You can follow our previous articles for MD...
We have provided several tutorials on molecular dynamics (MD) simulation (please check further reading section). They include installation of simulation software, simulation of a simple protein,...
Molecular dynamics (MD) simulation is one of the most widely used methods in bioinformatics. It needs high computation time and therefore, performed on workstations and servers....
GROMOS96 is a well-known software package used for biomolecular simulations [1]. It can be used for the molecular dynamics simulation of protein, peptide, and protein-ligand complex...
Molecular dynamics (MD) simulation is considered amongst the important methods in bioinformatics. Installation of MD simulation software and execution of their commands is critical. It requires...
This is a video tutorial of our existing article “Molecular Dynamics (MD) Simulation 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...
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...
