A1 Journal article (refereed)
Scalable Constant pH Molecular Dynamics in GROMACS (2022)

Aho, N., Buslaev, P., Jansen, A., Bauer, P., Groenhof, G., & Hess, B. (2022). Scalable Constant pH Molecular Dynamics in GROMACS. Journal of Chemical Theory and Computation, 18(10), 6148-6160. https://doi.org/10.1021/acs.jctc.2c00516

JYU authors or editors

Publication details

All authors or editors: Aho, Noora; Buslaev, Pavel; Jansen, Anton; Bauer, Paul; Groenhof, Gerrit; Hess, Berk

Journal or series: Journal of Chemical Theory and Computation

ISSN: 1549-9618

eISSN: 1549-9626

Publication year: 2022

Publication date: 21/09/2022

Volume: 18

Issue number: 10

Pages range: 6148-6160

Publisher: American Chemical Society (ACS)

Publication country: United States

Publication language: English

DOI: https://doi.org/10.1021/acs.jctc.2c00516

Publication open access: Openly available

Publication channel open access:

Publication is parallel published (JYX): https://jyx.jyu.fi/handle/123456789/83385

Abstract

Molecular dynamics (MD) computer simulations are used routinely to compute atomistic trajectories of complex systems. Systems are simulated in various ensembles, depending on the experimental conditions one aims to mimic. While constant energy, temperature, volume, and pressure are rather straightforward to model, pH, which is an equally important parameter in experiments, is more difficult to account for in simulations. Although a constant pH algorithm based on the λ-dynamics approach by Brooks and co-workers [Kong, X.; Brooks III, C. L. J. Chem. Phys.1996, 105, 2414–2423] was implemented in a fork of the GROMACS molecular dynamics program, uptake has been rather limited, presumably due to the poor scaling of that code with respect to the number of titratable sites. To overcome this limitation, we implemented an alternative scheme for interpolating the Hamiltonians of the protonation states that makes the constant pH molecular dynamics simulations almost as fast as a normal MD simulation with GROMACS. In addition, we implemented a simpler scheme, called multisite representation, for modeling side chains with multiple titratable sites, such as imidazole rings. This scheme, which is based on constraining the sum of the λ-coordinates, not only reduces the complexity associated with parametrizing the intramolecular interactions between the sites but also is easily extendable to other molecules with multiple titratable sites. With the combination of a more efficient interpolation scheme and multisite representation of titratable groups, we anticipate a rapid uptake of constant pH molecular dynamics simulations within the GROMACS user community.

Keywords: molecular dynamics; molecules; peptides; proteins; potential energy; reaction mechanisms

Free keywords: molecular mechanics; monomers; peptides and proteins; potential energy; reaction mechanisms

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Ministry reporting: Yes

Reporting Year: 2022

Preliminary JUFO rating: 2