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Replica-Exchange and Standard State Binding Free Energies with Grand Canonical Monte Carlo

Replica-Exchange and Standard State Binding Free Energies with Grand Canonical Monte Carlo
Replica-Exchange and Standard State Binding Free Energies with Grand Canonical Monte Carlo
The ability of grand canonical Monte Carlo (GCMC) to create and annihilate molecules in a given region greatly aids the identification of water sites and water binding free energies in protein cavities. However, acceptance rates without the application of biased moves can be low, resulting in large variations in the observed water occupancies. Here, we show that replica exchange of the chemical potential significantly reduces the variance of the GCMC data. This improvement comes at a negligible increase in computational expense when simulations comprise of runs at different chemical potentials. Replica exchange GCMC is also found to substantially increase of the precision of standard state water binding free energies as calculated with grand canonical integration, which has allowed us to address a missing standard state correction.
1549-9618
6373–6381
Ross, Gregory A.
65d26eec-983b-4ab8-9d1c-9bd3b027f6dd
Bruce Macdonald, Hannah E.
8e3f96bf-6806-4dc9-bd25-5b7a5325c7a7
Cave-Ayland, Christopher
0fac5a8c-02ac-4b42-857f-4b0288c9b125
Cabedo Martinez, Ana I.
5eaa5bcb-fef2-4c60-babe-c92d3a8b68a4
Essex, Jonathan W.
1f409cfe-6ba4-42e2-a0ab-a931826314b5
Ross, Gregory A.
65d26eec-983b-4ab8-9d1c-9bd3b027f6dd
Bruce Macdonald, Hannah E.
8e3f96bf-6806-4dc9-bd25-5b7a5325c7a7
Cave-Ayland, Christopher
0fac5a8c-02ac-4b42-857f-4b0288c9b125
Cabedo Martinez, Ana I.
5eaa5bcb-fef2-4c60-babe-c92d3a8b68a4
Essex, Jonathan W.
1f409cfe-6ba4-42e2-a0ab-a931826314b5

Ross, Gregory A., Bruce Macdonald, Hannah E., Cave-Ayland, Christopher, Cabedo Martinez, Ana I. and Essex, Jonathan W. (2017) Replica-Exchange and Standard State Binding Free Energies with Grand Canonical Monte Carlo. Journal of Chemical Theory and Computation, 12 (13), 6373–6381. (doi:10.1021/acs.jctc.7b00738).

Record type: Article

Abstract

The ability of grand canonical Monte Carlo (GCMC) to create and annihilate molecules in a given region greatly aids the identification of water sites and water binding free energies in protein cavities. However, acceptance rates without the application of biased moves can be low, resulting in large variations in the observed water occupancies. Here, we show that replica exchange of the chemical potential significantly reduces the variance of the GCMC data. This improvement comes at a negligible increase in computational expense when simulations comprise of runs at different chemical potentials. Replica exchange GCMC is also found to substantially increase of the precision of standard state water binding free energies as calculated with grand canonical integration, which has allowed us to address a missing standard state correction.

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Accepted/In Press date: 1 November 2017
e-pub ahead of print date: 1 November 2017
Published date: 1 November 2017

Identifiers

Local EPrints ID: 416034
URI: http://eprints.soton.ac.uk/id/eprint/416034
ISSN: 1549-9618
PURE UUID: 404c4181-9a7d-4a2d-ba3e-c3c386ce4e74
ORCID for Christopher Cave-Ayland: ORCID iD orcid.org/0000-0003-0942-8030
ORCID for Jonathan W. Essex: ORCID iD orcid.org/0000-0003-2639-2746

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Date deposited: 30 Nov 2017 17:30
Last modified: 07 Oct 2020 05:20

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Contributors

Author: Gregory A. Ross
Author: Hannah E. Bruce Macdonald
Author: Christopher Cave-Ayland ORCID iD
Author: Ana I. Cabedo Martinez

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