Dear Sir,
I have performed a protein-ligand simulation using GROMACS Tutorial: Protein-Ligand Complex.
I wan to learn how to do analysis. I have used this command for the calculation of RMSD : gmx rms -s em.tpr -f md_0_10_center.xtc -n index.ndx -tu ns -o rmsd_jz4.xvg
choosing “Backbone” for least-squares fitting and “LIG_Heavy” for the RMSD calculation.
I have attached my graph.
How to know that the calculated RMSD is about 0.1 nm (1 Å) ?
By looking at the graph i feel, that the ligand was stable for the first 10ns simulation, and later till 42ns was very unstable (showed a lot of fluctuations) and after that towards 50ns, it got stable.
Is it a good sign to proceed? how to analyze? Kindly help.