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MD Simulation

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

Dr. Muniba Faiza

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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.

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:

  1. Putty
  2. 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:

  1. Hostname
  2. Port number
  3. 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


 

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

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Dr. Muniba Faiza

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MD Simulation

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

Dr. Muniba Faiza

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MD Simulation

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

Dr. Muniba Faiza

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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…)

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