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Prediction of partition coefficients by multiscale hybrid atomic-level/coarse-grain simulations

Prediction of partition coefficients by multiscale hybrid atomic-level/coarse-grain simulations
Prediction of partition coefficients by multiscale hybrid atomic-level/coarse-grain simulations
Coarse-grain models are becoming an increasingly important tool in computer simulations of a wide variety of molecular processes. In many instances it is, however, desirable to describe key portions of a molecular system at the atomic level. There is therefore a strong interest in the development of simulation methodologies that allow representations of matter with mixed granularities in a multiscale fashion. We report here a strategy to conduct mixed atomic-level and coarse-grain simulations of molecular systems with a recently developed coarse-grain model. The methodology is validated by computing partition coefficients of small molecules described in atomic detail and solvated by water or octane, both of which are represented by coarse-grain models. Because the present coarse-grain force field retains electrostatic interactions, the simplified solvent particles can interact realistically with the all-atom solutes. The partition coefficients computed by this approach rival the accuracy of fully atomistic simulations and are obtained at a fraction of their computational cost. The present methodology is simple, robust and applicable to a wide variety of molecular systems.
free-energy, water models, molecular-dynamics, soft sticky dipole, force-field, side-chain analogs, liquid water, cyclohexane, solvation, proteins
1520-5207
657-660
Michel, J.
c7f80319-5846-4a87-87c8-2cdc4decf080
Orsi, M.
c5ff820a-f1cd-4486-b6dc-68e97c011e03
Essex, J.W.
1f409cfe-6ba4-42e2-a0ab-a931826314b5
Michel, J.
c7f80319-5846-4a87-87c8-2cdc4decf080
Orsi, M.
c5ff820a-f1cd-4486-b6dc-68e97c011e03
Essex, J.W.
1f409cfe-6ba4-42e2-a0ab-a931826314b5

Michel, J., Orsi, M. and Essex, J.W. (2008) Prediction of partition coefficients by multiscale hybrid atomic-level/coarse-grain simulations. The Journal of Physical Chemistry B, 112 (3), 657-660. (doi:10.1021/jp076142y).

Record type: Article

Abstract

Coarse-grain models are becoming an increasingly important tool in computer simulations of a wide variety of molecular processes. In many instances it is, however, desirable to describe key portions of a molecular system at the atomic level. There is therefore a strong interest in the development of simulation methodologies that allow representations of matter with mixed granularities in a multiscale fashion. We report here a strategy to conduct mixed atomic-level and coarse-grain simulations of molecular systems with a recently developed coarse-grain model. The methodology is validated by computing partition coefficients of small molecules described in atomic detail and solvated by water or octane, both of which are represented by coarse-grain models. Because the present coarse-grain force field retains electrostatic interactions, the simplified solvent particles can interact realistically with the all-atom solutes. The partition coefficients computed by this approach rival the accuracy of fully atomistic simulations and are obtained at a fraction of their computational cost. The present methodology is simple, robust and applicable to a wide variety of molecular systems.

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More information

Published date: 2008
Keywords: free-energy, water models, molecular-dynamics, soft sticky dipole, force-field, side-chain analogs, liquid water, cyclohexane, solvation, proteins

Identifiers

Local EPrints ID: 54484
URI: http://eprints.soton.ac.uk/id/eprint/54484
ISSN: 1520-5207
PURE UUID: b4f4c3b7-5f94-4ca9-933a-d24070aac967
ORCID for J.W. Essex: ORCID iD orcid.org/0000-0003-2639-2746

Catalogue record

Date deposited: 31 Jul 2008
Last modified: 03 Dec 2019 02:02

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