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 -o snapshot.pdb -dump <time>

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

$ gmx trjconv -f md_0_1.xtc -s md_0_1.tpr -o snapshot.pdb -dump 100

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 -o snapshots.pdb -b <time of first frame> -e <time of last frame>

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. SoftwareX, 1, 19-25.