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Extensive all-atom Monte Carlo sampling and QM/MM corrections in the SAMPL4 hydration free energy challenge

Extensive all-atom Monte Carlo sampling and QM/MM corrections in the SAMPL4 hydration free energy challenge
Extensive all-atom Monte Carlo sampling and QM/MM corrections in the SAMPL4 hydration free energy challenge
We present our predictions for the SAMPL4 hydration free energy challenge. Extensive all-atom Monte Carlo simulations were employed to sample the compounds in explicit solvent. While the focus of our study was to demonstrate well-converged and reproducible free energies, we attempted to address the deficiencies in the general Amber force field force field with a simple QM/MM correction. We show that by using multiple independent simulations, including different starting configurations, and enhanced sampling with parallel tempering, we can obtain well converged hydration free energies. Additional analysis using dihedral angle distributions, torsion-root mean square deviation plots and thermodynamic cycles support this assertion. We obtain a mean absolute deviation of 1.7 kcal mol(-1) and a Kendall's tau of 0.65 compared with experiment.
0920-654X
187-200
Genheden, Samuel
cc461200-48bd-411b-8424-23dfef65cc86
Cabedo Martinez, Ana I.
5eaa5bcb-fef2-4c60-babe-c92d3a8b68a4
Criddle, Michael P.
89fc3a00-a4ca-4416-a9a7-282d239bcdfd
Essex, Jonathan W.
1f409cfe-6ba4-42e2-a0ab-a931826314b5
Genheden, Samuel
cc461200-48bd-411b-8424-23dfef65cc86
Cabedo Martinez, Ana I.
5eaa5bcb-fef2-4c60-babe-c92d3a8b68a4
Criddle, Michael P.
89fc3a00-a4ca-4416-a9a7-282d239bcdfd
Essex, Jonathan W.
1f409cfe-6ba4-42e2-a0ab-a931826314b5

Genheden, Samuel, Cabedo Martinez, Ana I., Criddle, Michael P. and Essex, Jonathan W. (2014) Extensive all-atom Monte Carlo sampling and QM/MM corrections in the SAMPL4 hydration free energy challenge. Journal of Computer-Aided Molecular Design, 28 (3), 187-200. (doi:10.1007/s10822-014-9717-3). (PMID:24488307)

Record type: Article

Abstract

We present our predictions for the SAMPL4 hydration free energy challenge. Extensive all-atom Monte Carlo simulations were employed to sample the compounds in explicit solvent. While the focus of our study was to demonstrate well-converged and reproducible free energies, we attempted to address the deficiencies in the general Amber force field force field with a simple QM/MM correction. We show that by using multiple independent simulations, including different starting configurations, and enhanced sampling with parallel tempering, we can obtain well converged hydration free energies. Additional analysis using dihedral angle distributions, torsion-root mean square deviation plots and thermodynamic cycles support this assertion. We obtain a mean absolute deviation of 1.7 kcal mol(-1) and a Kendall's tau of 0.65 compared with experiment.

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More information

e-pub ahead of print date: 1 February 2014
Published date: March 2014
Organisations: Computational Systems Chemistry

Identifiers

Local EPrints ID: 395485
URI: http://eprints.soton.ac.uk/id/eprint/395485
ISSN: 0920-654X
PURE UUID: cbb733bc-f2f4-4ccf-8bdf-5e147342be38
ORCID for Jonathan W. Essex: ORCID iD orcid.org/0000-0003-2639-2746

Catalogue record

Date deposited: 31 May 2016 11:07
Last modified: 19 Nov 2019 01:59

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Contributors

Author: Samuel Genheden
Author: Ana I. Cabedo Martinez
Author: Michael P. Criddle

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