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복잡계 자기조립 연구단
복잡계 자기조립 연구단
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Constructing an Interpolated Potential Energy Surface of a Large Molecule: A Case Study with Bacteriochlorophyll a Model in the Fenna-Matthews-Olson Complex

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Title
Constructing an Interpolated Potential Energy Surface of a Large Molecule: A Case Study with Bacteriochlorophyll a Model in the Fenna-Matthews-Olson Complex
Author(s)
Chang Woo Kim; Young Min Rhee
Publication Date
2016-11
Journal
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, v.12, no.11, pp.5235 - 5246
Publisher
AMER CHEMICAL SOC
Abstract
Constructing a reliable potential energy surface (PES) is a key step toward computationally studying the chemical dynamics of any molecular system. The interpolation scheme is a useful tool that can closely follow the accuracy of quantum chemical means at a dramatically reduced computational cost. However, applying interpolation to building a PES of a large molecule is not a straightforward black-box approach, as it frequently encounters practical difficulties associated with its large dimensionality. Here, we present detailed courses of applying interpolation toward building a PES of a large chromophore molecule. We take the example of S0 and S1 electronic states of bacteriochlorophyll a (BChla) molecules in the Fenna-Matthews-Olson light harvesting complex. With a reduced model molecule that bears BChla's main π-conjugated ring, various practical approaches are designed for improving the PES quality in a stable manner and for fine-tuning the final surface such that the surface can be adopted for long time molecular dynamics simulations. Combined with parallel implementation, we show that interpolated mechanics/molecular mechanics (IM/MM) simulations of the entire complex in the nanosecond time scale can be conducted readily without any practical issues. With 1500 interpolation data points for each chromophore unit, the PES error relative to the reference quantum chemical calculation is found to be ∼0.15 eV in the thermally accessible region of the conformational space, together with ∼0.01 eV error in S0 - S1 transition energies. The performance issue related to the use of a large interpolation database within the framework of our parallel routines is also discussed. © 2016 American Chemical Society
URI
https://pr.ibs.re.kr/handle/8788114/2967
ISSN
1549-9618
Appears in Collections:
Center for Self-assembly and Complexity(복잡계 자기조립 연구단) > Journal Papers (저널논문)
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