Greeting After finishing a M.D simulation an ensuring that equilibration of the protein is done in its solvent cube according to RMS, potential energy ,temperature , pressure , radius of gyration ... etc what structure should i use for analysis ? is it the average structure of some few last nanoseconds of the simulation , OR the structure of the last frame in simulation, and is there any special cases where one of the two cited structures could insight more than the other ? ( for example : for Hydrogen bonds is the average structure more suitable for analysis than the last frame ? ...) Thanks :)
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