Connect with us

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.

For this purpose, we are going to use the gmx trjconv module of GROAMCS [1]. We will use the .xtc file as input.

$ gmx trjconv -f md_0_1.xtc -s md_0_1.tpr -dump <time> -o snapshot.pdb

For example, you want to extract a systems’ image at 100 ps, then the command will go like this:

$ gmx trjconv -f md_0_1.xtc -s md_0_1.tpr -dump <time> -o snapshot.pdb

Choose ‘system’ when prompted or any other appropriate option that you want to take a snapshot of.

If you want to take a snapshot between two times of frames, then use the following command.

$ gmx trjconv -f md_0_1.xtc -s md_0_1.tpr -b <time of first frame> -e <time of last frame> -o snapshots.pdb


References

  1. Abraham, M. J., Murtola, T., Schulz, R., Páll, S., Smith, J. C., Hess, B., & Lindahl, E. (2015). GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX1, 19-25.

Tariq is founder of Bioinformatics Review and CEO at IQL Technologies. His areas of expertise include algorithm design, phylogenetics, MicroArray, Plant Systematics, and genome data analysis. If you have questions, reach out to him via his homepage.

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

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

LATEST ISSUE

ADVERT