Thomas Potter thomas.d.potter@durham.ac.uk
PGR Student Doctor of Philosophy
Automated Coarse-Grained Mapping Algorithm for the Martini Force Field and Benchmarks for Membrane–Water Partitioning
Potter, Thomas D.; Barrett, Elin L.; Miller, Mark A.
Authors
Elin L. Barrett
Dr Mark Miller m.a.miller@durham.ac.uk
Associate Professor
Abstract
With a view to high-throughput simulations, we present an automated system for mapping and parameterizing organic molecules for use with the coarse-grained Martini force field. The method scales to larger molecules and a broader chemical space than existing schemes. The core of the mapping process is a graph-based analysis of the molecule’s bonding network, which has the advantages of being fast, general, and preserving symmetry. The parameterization process pays special attention to coarse-grained beads in aromatic rings. It also includes a method for building efficient and stable frameworks of constraints for molecules with structural rigidity. The performance of the method is tested on a diverse set of 87 neutral organic molecules and the ability of the resulting models to capture octanol–water and membrane–water partition coefficients. In the latter case, we introduce an adaptive method for extracting partition coefficients from free-energy profiles to take into account the interfacial region of the membrane. We also use the models to probe the response of membrane–water partitioning to the cholesterol content of the membrane.
Citation
Potter, T. D., Barrett, E. L., & Miller, M. A. (2021). Automated Coarse-Grained Mapping Algorithm for the Martini Force Field and Benchmarks for Membrane–Water Partitioning. Journal of Chemical Theory and Computation, 17(9), 5777-5791. https://doi.org/10.1021/acs.jctc.1c00322
Journal Article Type | Article |
---|---|
Acceptance Date | Aug 19, 2021 |
Online Publication Date | Sep 2, 2021 |
Publication Date | Sep 14, 2021 |
Deposit Date | Oct 30, 2021 |
Publicly Available Date | Dec 20, 2021 |
Journal | Journal of Chemical Theory and Computation |
Print ISSN | 1549-9618 |
Electronic ISSN | 1549-9626 |
Publisher | American Chemical Society |
Peer Reviewed | Peer Reviewed |
Volume | 17 |
Issue | 9 |
Pages | 5777-5791 |
DOI | https://doi.org/10.1021/acs.jctc.1c00322 |
Public URL | https://durham-repository.worktribe.com/output/1232048 |
Files
Published Journal Article
(2 Mb)
PDF
Publisher Licence URL
http://creativecommons.org/licenses/by/4.0/
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