Literature DB >> 18553900

Variance minimization of free energy estimates from optimized expanded ensembles.

Francisco J Martínez-Veracoechea1, Fernando A Escobedo.   

Abstract

We explored the possibility of improving the accuracy and precision of free-energy differences estimated via expanded ensembles by manipulation of the biasing weights. Three different weighing approaches were compared: the flat histogram (FH) method, the optimized ensemble (OE) method, and a method introduced in this work, denoted MinVar, which aims to explicitly minimize the expected variance. The performance of these three methods was tested for the simulation of chemical potentials in systems of symmetric diblock copolymers with chain lengths of either 10 or 4 beads, and a system of one large hard sphere of diameter 10 d immersed in a fluid of hard spheres of diameter d. In addition, the effect of the weighing method on the observed accuracy was investigated for different choices of macrostate staging and for both optimized and nonoptimized acceptance ratio methods for calculating free-energy differences. In the diblock copolymer systems, we found that the maximum attainable accuracy can be limited by correlations between the samples, causing the "real" observed variances to be much larger than the expected "ideal" ones. Hence, if the formal minimization of the variance, as aimed by the MinVar method, occurs at the expense of increasing the correlations in the data, the accuracy may actually decrease. Although maximizing the number of round trips between initial and final macrostates (as aimed by the OE method) was found to be directly related to data decorrelation, this only translates into increased accuracy if the correlations are the major source of errors in the free energy estimates. Finally, for the hard sphere system, we found that the MinVar method performs better than both the OE and FH methods even though the MinVar method in this case never completes a round trip, illustrating that maximizing the number of round trips for fixed computational cost does not necessarily lead to increased precision.

Entities:  

Year:  2008        PMID: 18553900     DOI: 10.1021/jp801688p

Source DB:  PubMed          Journal:  J Phys Chem B        ISSN: 1520-5207            Impact factor:   2.991


  3 in total

1.  SAMPL6 host-guest binding affinities and binding poses from spherical-coordinates-biased simulations.

Authors:  Zhaoxi Sun; Qiaole He; Xiao Li; Zhengdan Zhu
Journal:  J Comput Aided Mol Des       Date:  2020-01-23       Impact factor: 3.686

2.  Guidelines for the analysis of free energy calculations.

Authors:  Pavel V Klimovich; Michael R Shirts; David L Mobley
Journal:  J Comput Aided Mol Des       Date:  2015-03-26       Impact factor: 3.686

3.  Expanded Ensemble Methods Can be Used to Accurately Predict Protein-Ligand Relative Binding Free Energies.

Authors:  Si Zhang; David F Hahn; Michael R Shirts; Vincent A Voelz
Journal:  J Chem Theory Comput       Date:  2021-09-13       Impact factor: 6.578

  3 in total

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