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System-Specific Parameter Optimization for Nonpolarizable and Polarizable Force Fields
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DOI：10.1021/acs.jctc.3c01141.png)
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Abstract
En 中文
The accuracy of classical force fields (FFs) has been shown to be limited for the simulation of cation-protein systems despite their importance in understanding the processes of life. Improvements can result from optimizing the parameters of classical FFs or by extending the FF formulation by terms describing charge transfer (CT) and polarization (POL) effects. In this work, we introduce our implementation of the CTPOL model in OpenMM, which extends the classical additive FF formula by adding CT and POL. Furthermore, we present an open-source parametrization tool, called FFAFFURR, that enables the (system-specific) parametrization of OPLS-AA and CTPOL models. The performance of our workflow was evaluated by its ability to reproduce quantum chemistry energies and by molecular dynamics simulations of a zinc-finger protein.
Keywords:
MOLECULAR-DYNAMICS SIMULATIONS
INCLUDING CHARGE-TRANSFER
GLOBAL OPTIMIZATION
BINDING SITES
FREE-ENERGIES
METAL-IONS
PROTEINS
MECHANICS
APPROXIMATION
COORDINATION
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