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Molecular dynamics simulations of phosphatidylcholine membranes: a comparative force field study

Molecular dynamics simulations of phosphatidylcholine membranes: a comparative force field study
Molecular dynamics simulations of phosphatidylcholine membranes: a comparative force field study
Molecular dynamics simulations provide a route to studying the dynamics of lipid bilayers at atomistic or near atomistic resolution. Over the past 10 years or so, molecular dynamics simulations have become an established part of the biophysicist’s tool kit for the study of model biological membranes. As simulation time scales move from tens to hundreds of nanoseconds and beyond, it is timely to re-evaluate the accuracy of simulation models. We describe a comparative analysis of five freely available force fields that are commonly used to model lipid bilayers. We focus our analysis on 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) bilayers. We show that some bilayer properties have a pronounced force field dependence, while others are less sensitive. In general, we find strengths and weaknesses, with respect to experimental data, in all of the force fields we have studied. We do, however, find some combinations of simulation and force field parameters that should be avoided when simulating DPPC and POPC membranes. We anticipate that the results presented for some of the membrane properties will guide future improvements for several force fields studied in this work.
1549-9618
4593-4609
Piggot, Thomas J.
75829b71-d73b-43d1-b24f-3e70c2c4d0c8
Piñeiro, Ángel
7592e48b-ca8b-42a7-b57d-23d1581a8919
Khalid, Syma
90fbd954-7248-4f47-9525-4d6af9636394
Piggot, Thomas J.
75829b71-d73b-43d1-b24f-3e70c2c4d0c8
Piñeiro, Ángel
7592e48b-ca8b-42a7-b57d-23d1581a8919
Khalid, Syma
90fbd954-7248-4f47-9525-4d6af9636394

Piggot, Thomas J., Piñeiro, Ángel and Khalid, Syma (2012) Molecular dynamics simulations of phosphatidylcholine membranes: a comparative force field study. Journal of Chemical Theory and Computation, 8 (11), 4593-4609. (doi:10.1021/ct3003157).

Record type: Article

Abstract

Molecular dynamics simulations provide a route to studying the dynamics of lipid bilayers at atomistic or near atomistic resolution. Over the past 10 years or so, molecular dynamics simulations have become an established part of the biophysicist’s tool kit for the study of model biological membranes. As simulation time scales move from tens to hundreds of nanoseconds and beyond, it is timely to re-evaluate the accuracy of simulation models. We describe a comparative analysis of five freely available force fields that are commonly used to model lipid bilayers. We focus our analysis on 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) bilayers. We show that some bilayer properties have a pronounced force field dependence, while others are less sensitive. In general, we find strengths and weaknesses, with respect to experimental data, in all of the force fields we have studied. We do, however, find some combinations of simulation and force field parameters that should be avoided when simulating DPPC and POPC membranes. We anticipate that the results presented for some of the membrane properties will guide future improvements for several force fields studied in this work.

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More information

Published date: 27 August 2012
Organisations: Chemistry, Faculty of Natural and Environmental Sciences, Computational Systems Chemistry

Identifiers

Local EPrints ID: 352905
URI: http://eprints.soton.ac.uk/id/eprint/352905
ISSN: 1549-9618
PURE UUID: f11d83b1-a13c-4baa-b098-a4094f3c7376
ORCID for Syma Khalid: ORCID iD orcid.org/0000-0002-3694-5044

Catalogue record

Date deposited: 23 May 2013 14:47
Last modified: 03 Dec 2019 01:44

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