After doing virtual screening of the complex, i had done md simulation study of the protein-ligand complex for 40ns and i had got the curves. can anyone explain about their significance with respect to protein-ligand binding?
It is too early to interpret these charts; instead, let the MD simulations run longer to observe what happens. Those large discrepancies in your ligand-bound protein are caused by atom collisions or an unbalanced system.
Increase your simulation period as this much data is insufficient to conclude anything.......
During simulation it takes time for the system to get equilibrated ...... therefore more time is required to judge any results...
Regards
Sourav Majumdar It would be best to increase the simulation time, as it's too early to interpret these charts.
I agree with all but as per available data RMSDprotein (black colour) stable while complex (red colour) not stable only 4-5 ns.
RMSF indicate fluctuations that are less.
Radius of gyration Rg indicate compactness in graph complex and protein not compact thus not enough for activity.
SASA solvent surface accessible area also enogh supports