Developing Consistent Molecular Dynamics Force Fields for Biological Chromophores via Force Matching



Claridge, Kirsten and Troisi, Alessandro ORCID: 0000-0002-5447-5648
(2019) Developing Consistent Molecular Dynamics Force Fields for Biological Chromophores via Force Matching. JOURNAL OF PHYSICAL CHEMISTRY B, 123 (2). pp. 428-438.

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Abstract

The role of the environment in excitation energy transport in the pigment-protein complexes (PPCs) of photosynthetic organisms is a widely investigated topic. The spectral density is a key component in understanding this protein-pigment interaction; however, the typical approach for calculating spectral density, combining molecular dynamics with quantum chemistry (QC) calculations, suffers from the geometry mismatch problem, arising from the structural inconsistency between the force field (FF) and the QC calculation. Existing parameterization methods demand much time-consuming manual inputs, limiting the number of systems that can be studied. We present a method, utilizing force matching for the autoparameterization of new pigment FFs for the use in spectral density calculations of PPCs, and apply the method to three pigments. The use of these optimized FFs in spectral density computation results in a notable difference in comparison to the original FF.

Item Type: Article
Uncontrolled Keywords: Bacteria, Chlorophyll, Light-Harvesting Protein Complexes, Bacterial Proteins, Bacteriochlorophyll A, Quantum Theory, Molecular Dynamics Simulation, Chlorophyll Binding Proteins, Chlorophyll A
Depositing User: Symplectic Admin
Date Deposited: 28 Jan 2019 09:34
Last Modified: 19 Jan 2023 01:05
DOI: 10.1021/acs.jpcb.8b10746
Related URLs:
URI: https://livrepository.liverpool.ac.uk/id/eprint/3031872