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

Research paper by Kirsten K Claridge, Alessandro A Troisi

Indexed on: 20 Dec '18Published on: 20 Dec '18Published in: Journal of Physical Chemistry B



Abstract

The role of 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 of understanding this protein-pigment interaction, however the typical approach for calculating spectral density, combining molecular dynamics (MD) with quantum chemistry (QC) calculations, suffers from the geometry mismatch problem, arising from the structural inconsistency between the forcefield (FF) and the QC calculation. Existing parameterisation methods demand much time consuming manual input, limiting the number of systems that can be studied. We present a method, utilising force matching for the auto-parameterisation of new pigment FFs for the use in spectral density calculations of PPCs and apply the method to 3 pigments. The use of these optimised FFs in spectral density computation results in a notable difference in comparison to the original FF.