Literature DB >> 15197270

A simulation method for calculating the absolute entropy and free energy of fluids: 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 and free energy by analyzing Boltzmann samples obtained by Monte Carlo (MC) or molecular dynamics techniques. With HS applied to a fluid, each configuration i of the sample is reconstructed by adding its atoms gradually to the initially empty volume, i.e., by placing them in their positions at i using transition probabilities (TPs). At each step of the process, the volume is divided into two parts, the already visited part (the "past") and the "future" part, where obtaining the TP requires calculating partition functions over the future part in the presence of the frozen past. In recent publications, the TPs were calculated approximately by taking into account only partial future. Here we present a "complete HSMC" procedure, where the TPs are calculated from MC simulations carried out over the complete future. The complete HSMC method is applied to systems of liquid argon and the TIP3P model of water, and very good results for the free energy are obtained, as compared with results obtained by thermodynamic integration.

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Year:  2004        PMID: 15197270      PMCID: PMC438959          DOI: 10.1073/pnas.0308197101

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  7 in total

1.  Simulation method for calculating the entropy and free energy of peptides and proteins.

Authors:  Srinath Cheluvaraja; Hagai Meirovitch
Journal:  Proc Natl Acad Sci U S A       Date:  2004-06-14       Impact factor: 11.205

2.  Excess free energy of liquids from molecular dynamics simulations. Application to water models.

Authors:  J Hermans; A Pathiaseril; A Anderson
Journal:  J Am Chem Soc       Date:  1988-08-01       Impact factor: 15.419

Review 3.  Free energy via molecular simulation: applications to chemical and biomolecular systems.

Authors:  D L Beveridge; F M DiCapua
Journal:  Annu Rev Biophys Biophys Chem       Date:  1989

4.  Computer simulation of the free energy of polymer chains with excluded volume and with finite interactions.

Authors: 
Journal:  Phys Rev A Gen Phys       Date:  1985-12

5.  Dynamics of folded proteins.

Authors:  J A McCammon; B R Gelin; M Karplus
Journal:  Nature       Date:  1977-06-16       Impact factor: 49.962

6.  Stability of polypeptide conformational states as determined by computer simulation of the free energy.

Authors:  H Meirovitch; M Vásquez; H A Scheraga
Journal:  Biopolymers       Date:  1987-05       Impact factor: 2.505

Review 7.  Computer simulation of the free energy of peptides with the local states method: analogues of gonadotropin releasing hormone in the random coil and stable states.

Authors:  H Meirovitch; S C Koerber; J E Rivier; A T Hagler
Journal:  Biopolymers       Date:  1994-07       Impact factor: 2.505

  7 in total
  10 in total

1.  Simulation method for calculating the entropy and free energy of peptides and proteins.

Authors:  Srinath Cheluvaraja; Hagai Meirovitch
Journal:  Proc Natl Acad Sci U S A       Date:  2004-06-14       Impact factor: 11.205

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.  Optimization of the GB/SA solvation model for predicting the structure of surface loops in proteins.

Authors:  Agnieszka Szarecka; Hagai Meirovitch
Journal:  J Phys Chem B       Date:  2006-02-16       Impact factor: 2.991

5.  A black-box re-weighting analysis can correct flawed simulation data.

Authors:  F Marty Ytreberg; Daniel M Zuckerman
Journal:  Proc Natl Acad Sci U S A       Date:  2008-06-10       Impact factor: 11.205

6.  Absolute free energies and equilibrium ensembles of dense fluids computed from a nondynamic growth method.

Authors:  Divesh Bhatt; Daniel M Zuckerman
Journal:  J Chem Phys       Date:  2009-12-07       Impact factor: 3.488

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

9.  Extending fragment-based free energy calculations with library Monte Carlo simulation: annealing in interaction space.

Authors:  Steven Lettieri; Artem B Mamonov; Daniel M Zuckerman
Journal:  J Comput Chem       Date:  2010-11-29       Impact factor: 3.376

10.  Absolute free energies estimated by combining precalculated molecular fragment libraries.

Authors:  Xin Zhang; Artem B Mamonov; Daniel M Zuckerman
Journal:  J Comput Chem       Date:  2009-08       Impact factor: 3.376

  10 in total

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