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
- 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.
