I am a relatively new user to GROMACS (and MD in general), but I would like to fully understand how the ‘rms’ command performs its calculations.
In a say, 200ns simulation, where a mobile protein-ligand complex is simulated, I would like to measure the RMSD of the ligand relative to itself (where my reference file ligand is) and obtain the RMSD for each snapshot of the ligand to study the relative stability of the ligand within the binding pocket.
Does RMS account for the movement of the entire complex and the ligands relative position within the protein as it calculates the RMS with snapshot #1?
Or does it measure the RMSD of the starting position of only the ligand across the entirety of the simulation?
If you have any other advice on what I am trying to do that would be much appreciated.
You can separate choose the group to perform the fit on and one or more groups for computing the RMSD for.
I don’t understand what you mean with “the ligand relative to itself”. Is that when fitting on the ligand? That can be done. You can also fit on some protein atoms around to pocket to get the motion in the pocket.
Thank you Hess for the reply. Currently I am using 3 rms calculations with the following intentions.
rms ligand against ligand - to visualise any conformational changes in a relatively flexible small molecule
rms protein backbone against protein backbone - to visualise any large conformational changes in the protein throughout the simulation
rms ligand against protein backbone - to visualise any movements away from the initial starting position of the ligand at the start of the simulation.
When i overlay these 3 RMSD readings in one plot, is it possible to make the following deductions:
Ligand finds a more favourable binding site/conformation compared to starting position
Protein alters conformation in response to ligand binding
Could the shape of the 3 graphs in relation to one another indicate these sort of interactions? And if more information can be deduced from using these 3 readings?