Department of Applied Physics and Swedish e-Science Research Center, Science for Life Laboratory, KTH Royal Institute of Technology, 100 44 Stockholm, Sweden.
Nanoscience Center and Department of Chemistry, University of Jyväskylä, 40014 Jyväskylä, Finland.
J Chem Inf Model. 2024 Feb 12;64(3):567-574. doi: 10.1021/acs.jcim.3c01313. Epub 2024 Jan 12.
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.
恒 pH 值分子动力学（MD）是一种强大的技术，它允许残基的质子化状态动态变化，从而能够以前所未有的方式研究 pH 值依赖性。最近，一种恒 pH 值实现被整合到 GROMACS MD 包中。虽然这种实现提供了很好的准确性和性能，但需要手动修改和准备模拟输入文件，这可能很复杂、繁琐且容易出错。为了简化和自动化设置过程，我们介绍了 phbuilder，这是一个工具，它通过修改输入结构和拓扑结构以及生成必要的参数文件，为 GROMACS 自动准备恒 pH 值 MD 模拟。phbuilder 可以从初始结构和现有的模拟系统中准备恒 pH 值模拟，并且它还提供了进行滴定和新可滴定基团类型的单点参数化的功能。该工具可在 www.gitlab.com/gromacs-constantph 上免费获得。我们预计 phbuilder 将使恒 pH 值模拟更容易设置，从而使它们更容易被 GROMACS 用户社区使用。
