Literature DB >> 11456478

Why is it so difficult to simulate entropies, free energies, and their differences?

W P Reinhardt1, M A Miller, L M Amon.   

Abstract

The classical 19th century thermodynamic inequalities of Clausius and Helmholtz are applied to the calculation of entropy and free energy changes by computer simulation. The irreversibility of finite-time thermodynamic paths is exploited to obtain upper and lower bounds on these quantities. Schrödinger's microscopic interpretation of heat and work provides the basis for a literal implementation of the key historical concepts on the computer using the Monte Carlo algorithm of Metropolis. Coupling schemes, paths, and reference states are variationally optimized to improve the convergence of the simulated properties, and a newly introduced variational flexibility, metric scaling, is overviewed. Reasons for expecting limiting power laws for the convergence are outlined.

Mesh:

Year:  2001        PMID: 11456478     DOI: 10.1021/ar950181n

Source DB:  PubMed          Journal:  Acc Chem Res        ISSN: 0001-4842            Impact factor:   22.384


  7 in total

1.  Configurational entropy change of netropsin and distamycin upon DNA minor-groove binding.

Authors:  Jozica Dolenc; Riccardo Baron; Chris Oostenbrink; Joze Koller; Wilfred F van Gunsteren
Journal:  Biophys J       Date:  2006-05-26       Impact factor: 4.033

2.  Tetracycline-tet repressor binding specificity: insights from experiments and simulations.

Authors:  Alexey Aleksandrov; Linda Schuldt; Winfried Hinrichs; Thomas Simonson
Journal:  Biophys J       Date:  2009-11-18       Impact factor: 4.033

3.  On side-chain conformational entropy of proteins.

Authors:  Jinfeng Zhang; Jun S Liu
Journal:  PLoS Comput Biol       Date:  2006-12-08       Impact factor: 4.475

4.  Absolute Single-Molecule Entropies from Quasi-Harmonic Analysis of Microsecond Molecular Dynamics: Correction Terms and Convergence Properties.

Authors:  Riccardo Baron; Philippe H Hünenberger; J Andrew McCammon
Journal:  J Chem Theory Comput       Date:  2009-12-08       Impact factor: 6.006

Review 5.  Emerging methods for ensemble-based virtual screening.

Authors:  Rommie E Amaro; Wilfred W Li
Journal:  Curr Top Med Chem       Date:  2010       Impact factor: 3.295

6.  An improved relaxed complex scheme for receptor flexibility in computer-aided drug design.

Authors:  Rommie E Amaro; Riccardo Baron; J Andrew McCammon
Journal:  J Comput Aided Mol Des       Date:  2008-01-15       Impact factor: 3.686

7.  Independent-Trajectories Thermodynamic-Integration Free-Energy Changes for Biomolecular Systems: Determinants of H5N1 Avian Influenza Virus Neuraminidase Inhibition by Peramivir.

Authors:  Morgan Lawrenz; Riccardo Baron; J Andrew McCammon
Journal:  J Chem Theory Comput       Date:  2009-03-25       Impact factor: 6.006

  7 in total

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