Performance evaluation of the zero‐multipole summation method in modern molecular dynamics software

Sakuraba, Shun; Fukuda, Ikuo

doi:10.1002/jcc.25228

Cited by 10 publications

(9 citation statements)

References 58 publications

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“…Even with the commodity clusters, implementing efficient algorithms for accelerators enables microseconds simulations [5][6][7][8]. Moreover, theoretical developments in the mechanics and physics also accelerate MD simulations, e.g., efficient calculation methods for the electrostatic potential [9][10][11]. However, exploring the huge conformational spaces of complicated molecular systems is still not straightforward because the simulation trajectories are often trapped in energy basins and overlook rare events during the exploration of a rugged free-energy landscape.…”

Section: Introductionmentioning

confidence: 99%

myPresto/omegagene 2020: a molecular dynamics simulation engine for virtual-system coupled sampling

et al. 2020

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The molecular dynamics (MD) method is a promising approach for investigating the molecular mechanisms of microscopic phenomena. In particular, generalized ensemble MD methods can efficiently explore the conformational space with a rugged free-energy surface. However, the implementation and acquisition of technical knowledge for each generalized ensemble MD method are not straightforward for end-users. Here, we present a new version of the myPresto/omegagene software, which is an MD simulation engine tailored for a series of generalized ensemble methods, which are virtual-system coupled multicanonical MD (V-McMD), virtual-system coupled adaptive umbrella sampling (V-AUS), and virtual-system coupled canonical MD (VcMD). This program has been applied in several studies analyzing free-energy landscapes of a variety of molecular systems with all-atom simulations. The updated version provides new functionality for coarse-grained simulations powered by the hydrophobicity scale method. The software package includes a step-by-step tutorial document for enhanced conformational sampling of the poly-glutamine (poly-Q) oligomer expressed as a one-bead per residue model. The myPresto/omegagene software is freely available at the following URL: https://github.com/kotakasahara/omegagene under the Apache2 license.

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Section: Introductionmentioning

confidence: 99%

myPresto/omegagene 2020: a molecular dynamics simulation engine for virtual-system coupled sampling

et al. 2020

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“…The simulation time step was 2 fs. The zero-dipole method 38 , 39 was used to compute long-range electrostatic interactions. The cutoff distance for vdW and the electrostatic interaction was 12.0 Å.…”

Section: Methodsmentioning

confidence: 99%

Enzyme modification using mutation site prediction method for enhancing the regioselectivity of substrate reaction sites

Ikebe

Suzuki²,

Komori³

et al. 2021

Sci Rep

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Enzymes with low regioselectivity of substrate reaction sites may produce multiple products from a single substrate. When a target product is produced industrially using these enzymes, the production of non-target products (byproducts) causes adverse effects such as increased processing costs for purification and the amount of raw material. Thus it is required the development of modified enzymes to reduce the amount of byproducts’ production. In this paper, we report a method called mutation site prediction for enhancing the regioselectivity of substrate reaction sites (MSPER). MSPER takes conformational data for docking poses of an enzyme and a substrate as input and automatically generates a ranked list of mutation sites to destabilize docking poses for byproducts while maintaining those for target products in silico. We applied MSPER to the enzyme cytochrome P450 CYP102A1 (BM3) and the two substrates to enhance the regioselectivity for four target products with different reaction sites. The 13 of the total 14 top-ranked mutation sites predicted by MSPER for the four target products succeeded in selectively enhancing the regioselectivity up to 6.4-fold. The results indicate that MSPER can distinguish differences of substrate structures and the reaction sites, and can accurately predict mutation sites to enhance regioselectivity without selection by directed evolution screening.

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“…ZMM is a method that we and our collaborators have developed Mashimo et al 2013;Fukuda et al 2011Fukuda et al , 2014Kasahara et al 2016;Sakuraba and Fukuda 2018).…”

Section: Introductionmentioning

confidence: 99%

Non-Ewald methods for evaluating the electrostatic interactions of charge systems: similarity and difference

Fukuda

Nakamura

2022

Biophys Rev

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In molecular simulations, it is essential to properly calculate the electrostatic interactions of particles in the physical system of interest. Here we consider a method called the non-Ewald method, which does not rely on the standard Ewald method with periodic boundary conditions, but instead relies on the cuto¤-based techniques. We focus on the physicochemical and mathematical conceptual aspects of the method in order to gain a deeper understanding of the simulation methodology.In particular, we take into account the reaction …eld (RF) method, the isotropic periodic sum (IPS) method, and the zero-multipole summation method (ZMM). These cuto¤-based methods are based on di¤erent physical ideas and are completely distinguishable in their underlying concepts. The RF and IPS methods are "additive" methods that incorporate information outside the cuto¤ region, via dielectric medium and isotropic boundary condition, respectively. In contrast, the ZMM is a "subtraction" method that tries to remove the arti…cial e¤ects, generated near the boundary, from the cuto¤ sphere. Nonetheless, we …nd physical and/or mathematical similarities between these methods. In particular, the modi…ed RF method can be derived by the principle of neutralization utilized in the ZMM, and we also found a direct relationship between IPS and ZMM.

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Performance evaluation of the zero‐multipole summation method in modern molecular dynamics software

Cited by 10 publications

References 58 publications

myPresto/omegagene 2020: a molecular dynamics simulation engine for virtual-system coupled sampling

myPresto/omegagene 2020: a molecular dynamics simulation engine for virtual-system coupled sampling

Enzyme modification using mutation site prediction method for enhancing the regioselectivity of substrate reaction sites

Non-Ewald methods for evaluating the electrostatic interactions of charge systems: similarity and difference

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