Hi Tarun

Whenever you finished your simulation there are two GROMACS commands for analyzing hydrogen bonds and secondary structures.

For hydrogen bonds: g_hbond

http://manual.gromacs.org/current/online/g_hbond.html

For secondary structures along the simulation, I liked to use do_dssp command. This is basically a program that talks with DSSP software (you must install it) and reading the trajectory file computes an evolution of secondary structure elements in your protein along the simulation. Be careful because there are some compatibility problems in some DSSP versions. Here is the manual of do_dssp command:

http://manual.gromacs.org/current/online/do_dssp.html

About the differences between RMSD and RMSF, the RMSD is measured relative to the reference structure (i.e. the one present in the .tpr file). RMSF is measured with respect to average coordinates. I will use the backbone instead of the c-alpha because the information that you will get is more complete. However, it is difficult to relate this values with the stability of the protein without any further information. Some proteins are very flexible (will give you higher RMSD-RMSF fluctuations), but they are very stable.

Hope it helps. Best

Paco

For addition, you can observe the fluctuation of each residues in your protein for RMSF fluctuation. It measure the thermal motions of a residues and gives an overview on flexible regions in protein. Peaks indicated the most fluctuated area throughout simulation

In addition to previous answers, I would mention the following:

- RMSD is a parameter indicating the stability of the ENTIRE atom selection (e.g. protein backbone or trace) ALONG TIME. Usually it is used to evaluate when your system has reached an equilibrium (RMSD values no longer increase in time) and to estimate how long you should run a simulation (if RMSD values have been stable for several nanoseconds, it is safe to assume that you may stop the simulation). However, this parameter gives no indication on which part of the protein is more stable/variable.

- RMSF is the time-average of RMSD for EACH RESIDUE (this is why it is called also "RMSD-per-residue"). Usually core protein regions have low RMSF and exposed loops have high RMSF values.

For examples of the use of these parameters, please have a look at attached papers.:

Good luck!

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