Literature DB >> 15267955

Chaperoned alchemical free energy simulations: a general method for QM, MM, and QM/MM potentials.

Wei Yang1, Ryan Bitetti-Putzer, Martin Karplus.   

Abstract

A general method for alchemical free energy simulations using QM, MM, and QM/MM potential is developed by introducing "chaperones" to restrain the structures, particularly near the end points. A calculation of the free energy difference between two triazole tautomers in aqueous solution is used to illustrate the method. (c) 2004 American Institute of Physics.

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Year:  2004        PMID： 15267955     DOI： 10.1063/1.1738106

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


  6 in total

Review 1.  CHARMM: the biomolecular simulation program.

Authors:  B R Brooks; C L Brooks; A D Mackerell; L Nilsson; R J Petrella; B Roux; Y Won; G Archontis; C Bartels; S Boresch; A Caflisch; L Caves; Q Cui; A R Dinner; M Feig; S Fischer; J Gao; M Hodoscek; W Im; K Kuczera; T Lazaridis; J Ma; V Ovchinnikov; E Paci; R W Pastor; C B Post; J Z Pu; M Schaefer; B Tidor; R M Venable; H L Woodcock; X Wu; W Yang; D M York; M Karplus
Journal:  J Comput Chem       Date:  2009-07-30       Impact factor: 3.376

2.  Multiscale Monte Carlo Sampling of Protein Sidechains: Application to Binding Pocket Flexibility.

Authors:  Jerome Nilmeier; Matt Jacobson
Journal:  J Chem Theory Comput       Date:  2008-05       Impact factor: 6.006

3.  Calculating distribution coefficients based on multi-scale free energy simulations: an evaluation of MM and QM/MM explicit solvent simulations of water-cyclohexane transfer in the SAMPL5 challenge.

Authors:  Gerhard König; Frank C Pickard; Jing Huang; Andrew C Simmonett; Florentina Tofoleanu; Juyong Lee; Pavlo O Dral; Samarjeet Prasad; Michael Jones; Yihan Shao; Walter Thiel; Bernard R Brooks
Journal:  J Comput Aided Mol Des       Date:  2016-08-30       Impact factor: 3.686

4.  Dummy Atoms in Alchemical Free Energy Calculations.

Authors:  Markus Fleck; Marcus Wieder; Stefan Boresch
Journal:  J Chem Theory Comput       Date:  2021-06-14       Impact factor: 6.006

5.  Multiscale Free Energy Simulations: An Efficient Method for Connecting Classical MD Simulations to QM or QM/MM Free Energies Using Non-Boltzmann Bennett Reweighting Schemes.

Authors:  Gerhard König; Phillip S Hudson; Stefan Boresch; H Lee Woodcock
Journal:  J Chem Theory Comput       Date:  2014-02-11       Impact factor: 6.006

6.  A Comparison of QM/MM Simulations with and without the Drude Oscillator Model Based on Hydration Free Energies of Simple Solutes.

Authors:  Gerhard König; Frank C Pickard; Jing Huang; Walter Thiel; Alexander D MacKerell; Bernard R Brooks; Darrin M York
Journal:  Molecules       Date:  2018-10-19       Impact factor: 4.411
  6 in total

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