Hello,

I performed with Amber three replicas of a 1200 ns MD simulation on a protein dimer (wild type one), using the exact same parameters (except for the random seed that changes the initial velocities). I report here the RMSD (vs time [ps]) and the RMSF (vs residue number) of the three replicas.

It seems that the three RMSDs are quite stabilized at the and of the simulation, but regarding the RMSFs, the blue one is quite different from the red and yellow one. Considering that, in order to analyse the results and extract some correct information, which replica one do I have to choose? Do I need more replicas, more than 3? (Even though it seems that 1200ns simulations is enough for an MD simulation on a small protein dimer of 306 amino acids)

Beyond the three replicas of MD simulations made on the wild type dimer, I performed three MD simulations for other mutated dimers and I was looking for a way with MD simulations to evaluate differences between wild type and mutated dimers (maybe destabilization or more stabilization of the mutated ones, changing in conformations excetera.

Thank you very much