Rapid free energy calculations, approximate

A linear dependence approximately describes the results in a range of extraction times between 1 ps and 50 ps, and this extrapolates to a value of Ws not far from that observed for the 100 ps extractions. However, for the simulations with extraction times, tg > 50 ps, the work decreases more rapidly with l/tg, which indicates that the 100 ps extractions still have a significant frictional contribution. As additional evidence for this, we cite the statistical error in the set of extractions from different starting points (Fig. 2). As was shown by one of us in the context of free energy calculations[12], and more recently again by others specifically for the extraction process [1], the statistical error in the work and the frictional component of the work, Wp are related. For a simple system obeying the Fokker-Planck equation, both friction and mean square deviation are proportional to the rate, and... 

There now exist several methods for predicting the free energy associated with a compositional or conformational change.7 These can be crudely classified into two types "exact" and "approximate" free energy calculations. The former type, which we shall discuss in the following sections, is based directly on rigorous equations from classical statistical mechanics. The latter type, to be discussed later in this chapter, starts with statistical mechanics, but then combines these equations with assumptions and approximations to allow simulations to be carried out more rapidly. 

Angle brackets in Eqs. (31a) and (31b) denote averaging over the whole spectrum of the states of slow variables. Generally, the states of rapid variables depend on those of slow variables, so that SFj(a) and 8F (r a) cannot be taken out of the angle brackets. An expression in the quasichemical approximation for the free energy that are needed for calculation of the 8Fy(d) and 8F (r d) is given in Appendix A. 

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