Constant pH Simulation with FMM Electrostatics in GROMACS. (A) Design and Applications.

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Tác giả: Eliane Briand, Helmut Grubmüller, Bartosz Kohnke, Carsten Kutzner

Ngôn ngữ: eng

Ký hiệu phân loại: 809.008 History and description with respect to kinds of persons

Thông tin xuất bản: United States : Journal of chemical theory and computation , 2025

Mô tả vật lý:

Bộ sưu tập: NCBI

ID: 679561

The structural dynamics of biological macromolecules, such as proteins, DNA/RNA, or complexes thereof, are strongly influenced by protonation changes of their typically many titratable groups, which explains their sensitivity to pH changes. Conversely, conformational and environmental changes of the biomolecule affect the protonation state of these groups. With few exceptions, conventional force field-based molecular dynamics (MD) simulations neither account for these effects nor do they allow for coupling to a pH buffer. Here, we present design decisions and applications of a rigorous Hamiltonian interpolation λ-dynamics constant pH method in GROMACS, which rests on GPU-accelerated Fast Multipole Method (FMM) electrostatics. Our implementation supports both CHARMM36m and Amber99sb*-ILDN force fields and is largely automated to enable seamless switching from regular MD to constant pH MD, involving minimal changes to the input files. Here, the first of two companion papers describes the underlying constant pH protocol and sample applications to several prototypical benchmark systems such as cardiotoxin V, lysozyme, and staphylococcal nuclease. Enhanced convergence is achieved through a new dynamic barrier height optimization method, and high p
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