A1 Journal article (refereed)
phbuilder : A Tool for Efficiently Setting up Constant pH Molecular Dynamics Simulations in GROMACS (2024)

Jansen, A., Aho, N., Groenhof, G., Buslaev, P., & Hess, B. (2024). phbuilder : A Tool for Efficiently Setting up Constant pH Molecular Dynamics Simulations in GROMACS. Journal of Chemical Information and Modeling, 64(3), 567-574. https://doi.org/10.1021/acs.jcim.3c01313

JYU authors or editors

Publication details

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

Journal or series: Journal of Chemical Information and Modeling

ISSN: 1549-9596

eISSN: 1549-960X

Publication year: 2024

Publication date: 12/01/2024

Volume:  64

Issue number: 3

Pages range: 567-574

Publisher: American Chemical Society (ACS)

Publication country: United States

Publication language: English

DOI: https://doi.org/10.1021/acs.jcim.3c01313

Publication open access: Openly available

Publication channel open access: Partially open access channel

Publication is parallel published (JYX): https://jyx.jyu.fi/handle/123456789/92887

Abstract

Constant pH molecular dynamics (MD) is a powerful technique that allows the protonation state of residues to change dynamically, thereby enabling the study of pH dependence in a manner that has not been possible before. Recently, a constant pH implementation was incorporated into the GROMACS MD package. Although this implementation provides good accuracy and performance, manual modification and the preparation of simulation input files are required, which can be complicated, tedious, and prone to errors. To simplify and automate the setup process, we present phbuilder, a tool that automatically prepares constant pH MD simulations for GROMACS by modifying the input structure and topology as well as generating the necessary parameter files. phbuilder can prepare constant pH simulations from both initial structures and existing simulation systems, and it also provides functionality for performing titrations and single-site parametrizations of new titratable group types. The tool is freely available at www.gitlab.com/gromacs-constantph. We anticipate that phbuilder will make constant pH simulations easier to set up, thereby making them more accessible to the GROMACS user community.

Keywords: ions; molecules; peptides; proteins; mathematical methods

Free keywords: chemical structure; ions; mathematical methods; molecules; peptides; proteins

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Ministry reporting: Yes

VIRTA submission year: 2024

Preliminary JUFO rating: 1