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. Author manuscript; available in PMC: 2012 Dec 1.

Published in final edited form as: J Comput Chem. 2011 Sep 22;32(16):3505–3519. doi: 10.1002/jcc.21939

Calculations of diffusion coefficients for proteins in aqueous solution using the strategy of averaging MSD of multiple independent MD runs. Left panel: MSD ~ simulation time plots for 20 MD runs; right panel: correlation between mean MSD ~ simulation time. (a) 1BWI, (b) 1EX3, (c) 1HRC, and (d) 1OVA

Calculations of diffusion coefficients for proteins in aqueous solution using the strategy of averaging MSD of multiple independent MD runs. Left panel: MSD ~ simulation time plots for 20 MD runs; right panel: correlation between mean MSD ~ simulation time. (a) 1BWI, (b) 1EX3, (c) 1HRC, and (d) 1OVA