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

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.
Preparing system
On Ubuntu
Open a terminal (Ctrl+Alt+T) and log in to the server directly using the following command:
$ ssh -l username IP-address
You can use the scp command to copy files from your system to the server. For more details, type $ man scp
in a terminal.
On Windows
To run a job on a server using a Windows operating system, you need the following two software installed on your system:
- Putty
- WinSCP
Download the latest version of Putty from here according to your system architecture (whether 32-bit or 64-bit) and that of WinSCP from here.
Setting up the software
Install the software by double-clicking on the downloaded files. Open WinSCP and enter the following details:
- Hostname
- Port number
- Username (optional, you can enter it on the prompt as well).
After authentication, it will ask you for a password. Enter the password and log in. It will display two sections. One is your local computer (RHS) and another one is the server (LHS). Now, you can easily locate the directory on your system from where you want to copy files. Select the folder and drag and drop to the server-side.
Similarly, you need to set up Putty. Enter the above details and save the session for further use. Every time you open putty, just select the session and click ‘Load‘. It will open a blank screen asking for your login credentials (username and password).
Submitting a simulation job
You need a PBS script for that. This script specifies the number of nodes to be used for the job and the command to be run on the server. This script is provided by the service provider. Open the script and write the mdrun command wherever specified.
On Ubuntu
qsub command is used to submit a job using PBS script.
$ qsub script.pbs
On Windows
Open Putty and move inside the directory where you have kept all files.
$ qsub script.pbs
Remember to keep all files in the same folder.
Checking job status
To check the status of your submitted job, type the following command:
$ qstat
or
$ qstat -u user
MD Simulation
Energy minimization and equilibration of simple protein using NAMD & VMD.

In this tutorial, we will perform energy minimization and equilibration of a simple protein using NAMD [1] & VMD [2]. We are using insulin (PDB ID: 2wfu) for this tutorial.
MD Simulation
Generating topology of molecule for AMBER forcefield for GROMACS.

In this article, we will generate the topology of a small molecule for AMBER forcefield to be used in MD simulation using GROMACS.
MD Simulation
How to visualize output plots of MD simulation (GROMACS)?

Visualizing plots of molecular dynamics simulation is easy once you have generated them. Previously, we provided a few articles on MD output analysis (check the Further Reading section). This article explains how you can easily visualize the plots generated from GROMACS output. (more…)
MD Simulation
How to solve ‘Could NOT find CUDA: Found unsuitable version “10.1”‘ error during GROMACS installation?

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 frequently occurring during GROMACS installation.
MD Simulation
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. (more…)
MD Simulation
How to install 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…)
MD Simulation
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…)
MD Simulation
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…)
MD Simulation
Easy installation of GROMACS on Ubuntu 18.04 & 20.04

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…)
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
How to 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…)
MD Simulation
Tutorial: MD Simulation of small organic molecules using GROMACS

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…)
MD Simulation
Tutorial: MD simulation with mixed solvents using GROMACS

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…)
MD Simulation
Tutorial: 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…)
MD Simulation
Method-1: Installing GROMACS on Ubuntu with CUDA GPU Support

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…)
MD Simulation
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…)
MD Simulation
MD Simulation using GROMACS: Things to remember

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…)
MD Simulation
Video Tutorial: MD Simulation using GROMACS

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