Connect with us

MD Simulation

How to calculate number of steps (nsteps) for MD simulation run?

Published

on

How to calculate number of steps (nsteps) for MD simulation run?

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, we will learn to calculate nsteps for an MD run.

When we prepare the MD run file (md.mdp) in the GROMACS simulation, we need to write the exact number of steps depending on the length of the simulation in nanoseconds (ns). How many ns a simulation will run is determined by providing the nsteps in the md.mdp file. That’s how we do it.

For 1 ns simulation

Let’s assume time in ns is and 1000 ps = 1 ns, therefore, the general equation will be:

nsteps * timestep (ps/step) = 1000 * x ps = x ns

So, if you want to run MD for 1 ns, then the equation will be,

x (nsteps) * 0.002 time (ps/step) = 1 ns ###The timestep in production MD runs (dT) is 2 fs (i.e., 0.002 ps).

x (nsteps)  = 1 ns/ 0.002 time (ps/step)

x (nsteps)  =  500

500 (nsteps) * 0.002 time (ps/step) = 1 ns

The number of steps for a 1 ns simulation will be 500.

For 100 ns simulation

If you want to run an MD simulation for 100ns, then the equation will become like this:

x (nsteps) * 0.002 time (ps/step) = 100 ns ###The timestep in production MD runs (dT) is 2 fs (i.e., 0.002 ps).

x (nsteps)  = 100 ns/ 0.002 time (ps/step)

x (nsteps)  =  50000

50000 (nsteps) * 0.002 time (ps/step) = 100 ns

The number of steps for 100 ns simulation will be 50000.


 

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

MD Simulation

How to install GROMACS on Apple M1 (MacOS)?

Published

on

Installing GROMACS on Apple M1 (MacOS)

We have provided a few articles on GROMACS installation on Ubuntu. In this article, we are going to install GROMACS [1] on Mac OS. (more…)

Continue Reading

MD Simulation

How to take snapshots of structure at specific times in GROMACS?

Published

on

How to take snapshots of structure at specific times in GROMACS?

It is important to see the behavior of protein during an MD simulation. This can be achieved by taking snapshots in the form of PDB format. In this article, we have provided a few commands that you can use to take snapshots of a complete system or protein during MD simulation. (more…)

Continue Reading

MD Simulation

GROMACS: Uses & Applications

Published

on

GROMACS: Uses & Applications

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 generally used for molecular dynamics simulation of macromolecules. In this article, we will explain its uses and applications in bioinformatics studies. (more…)

Continue Reading

MD Simulation

Easy installation of GROMACS on Ubuntu 18.04 & 20.04

Published

on

Installing GROMACS on ubuntu

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 shell scripts to install the latest (2021 series) of GROMACS on Ubuntu 18.04 and 20.04. (more…)

Continue Reading

MD Simulation

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

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

How to generate topology of small molecules & ligands for MD Simulation?

Published

on

generate topology of small molecules & ligands for MD simulation

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 tutorials. In this article, we will explain how can you generate the topology of ligands for MD simulation of complex or small molecules only. (more…)

Continue Reading

MD Simulation

Tutorial: MD Simulation of small organic molecules using GROMACS

Published

on

MD Simulation of small molecules

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 small organic molecules. (more…)

Continue Reading

MD Simulation

Tutorial: MD simulation with mixed solvents using GROMACS

Published

on

MD simulation with mixed solvents

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 simulation of a simple protein and a protein-ligand complex. (more…)

Continue Reading

MD Simulation

Tutorial: MD simulation output analysis of a complex using GROMACS

Published

on

MD simulation output analysis of a complex using GROMACS

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, and a complex. In this article, we will analyze the GROMACS [1] output of MD simulation of a complex. (more…)

Continue Reading

MD Simulation

How to submit MD simulation job on a cluster server using PBS script?

Published

on

MD Simulation on cluster server

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. It requires software to upload and download files to and from the server. In this article, we have explained how to submit MD simulation jobs on cluster computers using PBS scripts. (more…)

Continue Reading

MD Simulation

Method-1: Installing GROMACS on Ubuntu with CUDA GPU Support

Published

on

Install gromacs with gpu acceleration

GROMACS [1] is one of the most popular software in bioinformatics for molecular dynamic (MD) studies of macromolecules. We have provided different tutorials regarding MD simulation using GROMACS including its installation on Ubuntu. In this article, we will install GROMACS with GPU acceleration. (more…)

Continue Reading

MD Simulation

Installing GROMOS96 on Ubuntu

Published

on

Installing gromos96 on Ubuntu

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 as well. In this article, we will install GROMOS96 on Ubuntu. (more…)

Continue Reading

MD Simulation

MD Simulation using GROMACS: Things to remember

Published

on

MD Simulation

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 several parameters to be considered before performing simulations. A single mistake may result in impractical outputs. In this article, we will discuss such important things to remember during the MD simulation and installation and execution of its software (GROMACS) [1,2]. (more…)

Continue Reading

MD Simulation

Video Tutorial: MD Simulation using GROMACS

Published

on

Video Tutorial: MD simulation using GROMACS

This is a video tutorial of our existing article “Molecular Dynamics (MD) Simulation using GROMACS“.

Continue Reading

MD Simulation

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

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

MD Simulation

Tutorial: A quick MD simulation using NAMD and VMD

Published

on

qwikmd

Molecular dynamics (MD) simulation has become an important methodology in research covering systems consisting of millions of atoms. We have provided several articles on MD simulation including the GROMACS [1] installation and performing MD. In this article, we will learn about “QwikMD” a plugin in NAMD [3], and VMD [4]. (more…)

Continue Reading

MD Simulation

Tutorial: MD simulation output analysis of protein using GROMACS

Published

on

Molecular dynamics (MD) simulation is an important step in studying the dynamics of macromolecules. In one of the previous articles, MD simulation of chain A of insulin (PDB ID: 1ZNI) was performed using GROMACS. The output analysis of that simulation is explained in this article. (more…)

Continue Reading

LATEST ISSUE

ADVERT