Free energy simulations: use of reverse cumulative averaging to determine the equilibrated region and the time required for convergence.
A method is proposed for improving the accuracy and efficiency of free energy simulations. The essential idea is that the convergence of the relevant measure (e.g., the free energy derivative in thermodynamic integration) is monitored in the reverse direction starting from the last frame of the trajectory, instead of the usual approach, which begins with the first frame and goes in the forward direction. This simple change in the use of the simulation data makes it straightforward to eliminate the contamination of the averages by contributions from the equilibrating region. A statistical criterion is introduced for distinguishing the equilibrated (production) region from the equilibrating region. The proposed method, called reverse cumulative averaging, is illustrated by its application to the well-studied case of the alchemical free energy simulation of ethane to methanol.
Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA.
Wei
W
Yang
Ryan
R
Bitetti-Putzer
Martin
M
Karplus
D003198:Computer Simulation; D004735:Energy Transfer; D004980:Ethane / Q000737:chemistry*; D007700:Kinetics; D008697:Methane / Q000737:chemistry*; D008956:Models, Chemical; D008958:Models, Molecular; D015233:Models, Statistical; D013997:Time Factors
D004980:Ethane; D008697:Methane