The University of Southampton
University of Southampton Institutional Repository

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.

This record has no associated files available for download.

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: 16 Mar 2024 02:45

Export record

Altmetrics

Contributors

Author: J. Michel
Author: M. Orsi
Author: J.W. Essex ORCID iD

Download statistics

Downloads from ePrints over the past year. Other digital versions may also be available to download e.g. from the publisher's website.

View more statistics

Atom RSS 1.0 RSS 2.0

Contact ePrints Soton: eprints@soton.ac.uk

ePrints Soton supports OAI 2.0 with a base URL of http://eprints.soton.ac.uk/cgi/oai2

This repository has been built using EPrints software, developed at the University of Southampton, but available to everyone to use.

We use cookies to ensure that we give you the best experience on our website. If you continue without changing your settings, we will assume that you are happy to receive cookies on the University of Southampton website.

×