Literature DB >> 15634040

Lower and upper bounds for the absolute free energy by the hypothetical scanning Monte Carlo method: application to liquid argon and water.

Ronald P White1, Hagai Meirovitch.   

Abstract

The hypothetical scanning (HS) method is a general approach for calculating the absolute entropy S and free energy F by analyzing Boltzmann samples obtained by Monte Carlo or molecular dynamics techniques. With HS applied to a fluid, each configuration i of the sample is reconstructed by gradually placing the molecules in their positions at i using transition probabilities (TPs). At each step of the process the system is divided into two parts, the already treated molecules (the "past"), which are fixed, and the as yet unspecified (mobile) "future" molecules. Obtaining the TP exactly requires calculating partition functions over all positions of the future molecules in the presence of the frozen past, thus it is customary to invoke various approximations to best represent these quantities. In a recent publication [Proc. Natl. Acad. Sci. USA 101, 9235 (2004)] we developed a version of HS called complete HSMC, where each TP is calculated from an MC simulation involving all of the future molecules (the complete future); the method was applied very successfully to Lennard-Jones systems (liquid argon) and a box of TIP3P water molecules. In its basic implementation the method provides lower and upper bounds for F, where the latter can be evaluated only for relatively small systems. Here we introduce a new expression for an upper bound, which can be evaluated for larger systems. We also propose a new exact expression for F and verify its effectiveness. These free energy functionals lead to significantly improved accuracy (as applied to the liquid systems above) which is comparable to our thermodynamic integration results. We formalize and discuss theoretical aspects of HSMC that have not been addressed in previous studies. Additionally, several functionals are developed and shown to provide the free energy through the analysis of a single configuration. (c) 2004 American Institute of Physics.

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Year:  2004        PMID: 15634040     DOI: 10.1063/1.1814355

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  15 in total

1.  Absolute free energy of binding of avidin/biotin, revisited.

Authors:  Ignacio J General; Ralitsa Dragomirova; Hagai Meirovitch
Journal:  J Phys Chem B       Date:  2012-02-27       Impact factor: 2.991

2.  Calculation of the entropy of random coil polymers with the hypothetical scanning Monte Carlo method.

Authors:  Ronald P White; Hagai Meirovitch
Journal:  J Chem Phys       Date:  2005-12-01       Impact factor: 3.488

3.  Calculation of the entropy and free energy from monte carlo simulations of a peptide stretched by an external force.

Authors:  Srinath Cheluvaraja; Hagai Meirovitch
Journal:  J Phys Chem B       Date:  2005-11-24       Impact factor: 2.991

4.  Minimalist explicit solvation models for surface loops in proteins.

Authors:  Ronald P White; Hagai Meirovitch
Journal:  J Chem Theory Comput       Date:  2006       Impact factor: 6.006

5.  Relative stability of the open and closed conformations of the active site loop of streptavidin.

Authors:  Ignacio J General; Hagai Meirovitch
Journal:  J Chem Phys       Date:  2011-01-14       Impact factor: 3.488

6.  Calculation of the Entropy of Lattice Polymer Models from Monte Carlo Trajectories.

Authors:  Ronald P White; Jason Funt; Hagai Meirovitch
Journal:  Chem Phys Lett       Date:  2005-07-20       Impact factor: 2.328

7.  Entropy and Free Energy of a Mobile Loop Based on the Crystal Structures of the Free and Bound Proteins.

Authors:  Mihail Mihailescu; Hagai Meirovitch
Journal:  Entropy (Basel)       Date:  2010-08-25       Impact factor: 2.524

8.  Free volume hypothetical scanning molecular dynamics method for the absolute free energy of liquids.

Authors:  Ronald P White; Hagai Meirovitch
Journal:  J Chem Phys       Date:  2006-05-28       Impact factor: 3.488

Review 9.  Methods for calculating the entropy and free energy and their application to problems involving protein flexibility and ligand binding.

Authors:  Hagai Meirovitch; Srinath Cheluvaraja; Ronald P White
Journal:  Curr Protein Pept Sci       Date:  2009-06       Impact factor: 3.272

10.  Molecular dynamic analysis of mutant Y195I α-cyclodextrin glycosyltransferase with switched product specificity from α-cyclodextrin to γ-cyclodextrin.

Authors:  Fangjin Chen; Ting Xie; Yang Yue; Shijun Qian; Yapeng Chao; Jianfeng Pei
Journal:  J Mol Model       Date:  2015-07-28       Impact factor: 1.810

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