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Reference 5, p 82. Note that definitions of g(r) and W(r) differ only by a multiplying factor which can be incorporated into the constant in eq 1. Therefore, all the formalism for g(r) would be equally valid for deriving an expression for W(r).
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Reference 5, p 82. Note that definitions of g(r) and W(r) differ only by a multiplying factor which can be incorporated into the constant in eq 1. Therefore, all the formalism for g(r) would be equally valid for deriving an expression for W(r).
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It was observed that the adjustment of the B parameter needs long test simulations and that the convergence characteristics of the average number of molecules calculated in a run with a "well" tuned B parameter may be rather slow. Although these effects have been observed to be small, they will still contribute to the thermodynamic state mismatches.
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85033052889
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Since the biasing function is regularly updated, simple error analysis methods such as block averages are not feasible in the adaptive umbrella sampling technique. Therefore, the convergence of the calculations is decided on by comparing the successive iterations, and the simulations are continued until the changes in pmf after the successive iterations are smaller than a certain value. The estimated statistical error for the LJ-LJ pmf is ; approximately 0.4 kcalmol, and it is approximately 0.7 kcalmol for the Na-Cl case.
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These small deviations from the targeted average number of molecules can actually be further corrected by the fine adjustment of the parameter.
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These small deviations from the targeted average number of molecules can actually be further corrected by the fine adjustment of the parameter.
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Different water models are used in these two cases, TIP4P vs TIPS2, so a direct comparison is not actually appropriate.
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Different water models are used in these two cases, TIP4P vs TIPS2, so a direct comparison is not actually appropriate.
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