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phbuilder: A Tool for Efficiently Setting up Constant pH Molecular Dynamics Simulations in GROMACS

Authors: Jansen, Anton; Aho, Noora; Groenhof, Gerrit; Buslaev, Pavel; Hess, Berk;

phbuilder: A Tool for Efficiently Setting up Constant pH Molecular Dynamics Simulations in GROMACS

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 not 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 preparation of simulation input files is required, which can be complicated, tedious, and error-prone. To simplify and automate the setup process, we present phbuilder, a tool that automatically prepares constant pH 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 initial protein structures as well as by converting existing simulation runs. phbuilder also provides functionality for performing titrations and parameterizing 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 and thereby more accessible to the GROMACS user community.

Country
Finland
Keywords

ionit, Organic Chemistry, Fysikaalinen kemia, mathematical methods, matemaattiset menetelmät, molekyylit, Molecular Dynamics Simulation, Hydrogen-Ion Concentration, Physical Chemistry, proteins, Orgaaninen kemia, peptidit, Nanoscience Center, chemical structure, ions, peptides, molecules, proteiinit, Software

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    This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
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selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
48
Top 1%
Top 10%
Top 1%
Green
hybrid