"TIME SENSITIVE-URGENT"
I am running an MD simulation for an atomistic model with NAMD. I want to know the uses of plotting an RMSD curve for the equilibrated model. Is it only used for equilibration, or does it reveal anything else on the model? Your valuable insights are welcome.
Small molecules may have some impact on the stability of the protein. Some papers may claim that the mean absolute RMSD value of the protein backbone during the MDs lower than 2 A indicates the protein-ligand complexes were stable. However, I think we should focus on the variation of the RMSD value rather than its mean value. If the variation is slight, it indicates that there are small conformation changes in the protein; hence the complexes are stable.
Nevertheless, I think that the RMSD plot not telling much, as most of the proteins from RCSB are in their natural form, therefore there will not be many transformations between its initial and equilibrated conformation.
Dear @Hari prasadh, I used Schrodinger software for MDS provided by Schrodinger team. RMSD plot talks about the stability of both protein and ligand. When you subject Protein-Ligand complex for MD analysis for 50 ns 100 ns etc, it produces a output of RMSD plot(Ligand on one side and Protein on another side) which shows the deviation occuring during the period of simulation. As per my knowledge and in many publications authors have mentioned that the deviation which occurs below 4 A⁰ forms a stable Protein ligand complex. It's just outline of RMSD. And many more can be withdrawn from MDS such as RMSF and residual interactions.
As highlighted in the above answers, RMSD is an indicator of the stability of the protein-complex and should be less than 2Å, but less than 3Å is still acceptable. Your curve should show minimal fluctuations near the end of the simulation time. Otherwise, if the curve is still rising, that's usually an indicator that a longer simulation time is needed.
However, on its own RMSD is not much use and should be combined with other data such as RMSF, H-bonds,Rg, PCA and free energy calculations to gain a deeper knowledge on the stability and viability of the investigated protein-ligand complex.
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