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Large-scale DFT calculations in implicit solvent-A case study on the T4 lysozyme L99A/M102Q protein

Large-scale DFT calculations in implicit solvent-A case study on the T4 lysozyme L99A/M102Q protein
Large-scale DFT calculations in implicit solvent-A case study on the T4 lysozyme L99A/M102Q protein
Recently, variants of implicit solvation models for first principles electronic structure calculations based on a direct solution of the nonhomogeneous Poisson equation in real space have been developed.These implicit solvation models are very elegant from a physical point of view as the solute cavity is defined directly via isosurfaces of the electronic density, and the molecular charge is
polarized self-consistently by the reaction field of the dielectric continuum which surrounds the solute. Nevertheless, the implementation of these models is technically complex and requires great care. A certain level of care is required from users of such models as a number of numerical parameters need to be given appropriate values to obtain the most accurate and physically relevant
results.Here,we describe in what parts of the solventmodel
each of these numerical parameters is involved and present a
detailed study of how they can affect the calculation, using the solvation model which has been implemented in the ONETEP program for linear-scaling density functional theory (DFT) calculations. As ONETEP is capable of DFT calculations with thousands of atoms, we focus our investigation of the numerical parameters with a case study on protein–ligand complexes of the entire 2602-atom T4 Lysozyme L99/M102Q protein.We examine effects on solvation energies and binding energies, which are critical
quantities for computational drug optimization and other types of biomolecular simulations.We propose optimal choices of these parameters suitable for routine “production” calculations.
0020-7608
771-785
Dziedzic, Jacek
8e2fdb55-dade-4ae4-bf1f-a148a89e4383
Fox, Stephen J.
a8957e8a-3086-4917-8575-eb0f9e8604cf
Fox, Thomas
04c97900-df28-4af0-a7ca-62e5efcfcaba
Tautermann, Christofer S.
f35b4fb9-df35-4e57-8d68-8e20b5a177fd
Skylaris, Chris-Kriton
8f593d13-3ace-4558-ba08-04e48211af61
Dziedzic, Jacek
8e2fdb55-dade-4ae4-bf1f-a148a89e4383
Fox, Stephen J.
a8957e8a-3086-4917-8575-eb0f9e8604cf
Fox, Thomas
04c97900-df28-4af0-a7ca-62e5efcfcaba
Tautermann, Christofer S.
f35b4fb9-df35-4e57-8d68-8e20b5a177fd
Skylaris, Chris-Kriton
8f593d13-3ace-4558-ba08-04e48211af61

Dziedzic, Jacek, Fox, Stephen J., Fox, Thomas, Tautermann, Christofer S. and Skylaris, Chris-Kriton (2013) Large-scale DFT calculations in implicit solvent-A case study on the T4 lysozyme L99A/M102Q protein. International Journal of Quantum Chemistry, 113 (6), 771-785. (doi:10.1002/qua.24075).

Record type: Article

Abstract

Recently, variants of implicit solvation models for first principles electronic structure calculations based on a direct solution of the nonhomogeneous Poisson equation in real space have been developed.These implicit solvation models are very elegant from a physical point of view as the solute cavity is defined directly via isosurfaces of the electronic density, and the molecular charge is
polarized self-consistently by the reaction field of the dielectric continuum which surrounds the solute. Nevertheless, the implementation of these models is technically complex and requires great care. A certain level of care is required from users of such models as a number of numerical parameters need to be given appropriate values to obtain the most accurate and physically relevant
results.Here,we describe in what parts of the solventmodel
each of these numerical parameters is involved and present a
detailed study of how they can affect the calculation, using the solvation model which has been implemented in the ONETEP program for linear-scaling density functional theory (DFT) calculations. As ONETEP is capable of DFT calculations with thousands of atoms, we focus our investigation of the numerical parameters with a case study on protein–ligand complexes of the entire 2602-atom T4 Lysozyme L99/M102Q protein.We examine effects on solvation energies and binding energies, which are critical
quantities for computational drug optimization and other types of biomolecular simulations.We propose optimal choices of these parameters suitable for routine “production” calculations.

Full text not available from this repository.

More information

Accepted/In Press date: 28 March 2012
Published date: 15 March 2013
Organisations: Chemistry, Faculty of Natural and Environmental Sciences, Computational Systems Chemistry

Identifiers

Local EPrints ID: 365356
URI: http://eprints.soton.ac.uk/id/eprint/365356
ISSN: 0020-7608
PURE UUID: 0676480f-b235-4676-a4ca-b73afcfa028d
ORCID for Jacek Dziedzic: ORCID iD orcid.org/0000-0003-4786-372X
ORCID for Chris-Kriton Skylaris: ORCID iD orcid.org/0000-0003-0258-3433

Catalogue record

Date deposited: 03 Jun 2014 10:48
Last modified: 12 Nov 2019 01:46

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