I have a 290+ residue protein and I recently ran a 200 ps simulation in a water box with electrostatic cutoff at approximately half the value of the box dimension. Since there is no heating stage in the dynamics, I am wondering what guidelines there are for knowing when to evaluate data from the simulation. There are some interesting features to the RMSD plot I would like to investigate. But I am not sure I can analyze the last 100 ps of the dynamics or not. Any help would be greatly appreciated.
Thanks! Mark
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