Critical test of isotropic periodic sum techniques with group-based cut-off schemes

Nozawa, Takuma; Yasuoka, Kenji; Takahashi, Kazuaki Z.

doi:10.1038/s41598-018-22514-3

Cited by 6 publications

(6 citation statements)

References 61 publications

(71 reference statements)

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“…As a result, the cost of the calculation of forces or potential is reduced to . ISF, which is the same as the Coulomb force, also called the long-range interaction, can be calculated in a similar manner to the short-range interaction using the linear-combination-based isotropic periodic sum switch (LIPS-SW) algorithm . We used this algorithm for all our experiments.…”

Section: Resultsmentioning

confidence: 99%

“…ISF, which is the same as the Coulomb force, also called the long-range interaction, can be calculated in a similar manner to the short-range interaction using the linear-combination-based isotropic periodic sum switch (LIPS-SW) algorithm. 29 We used this algorithm for all our experiments. Because LIPS-SW is an approximate potential, we used the correction using the instantaneous change in eq 5 calculated using numerical integration to maintain an unbiased MC simulation (the details are provided in Appendix S9).…”

Section: T H I S C O N T E N T Imentioning

confidence: 99%

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Efficient Monte Carlo Sampling for Molecular Systems Using Continuous Normalizing Flow

Endo

Yuhara

Yasuoka

2022

J. Chem. Theory Comput.

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Carlo molecular simulation is a powerful computational method for simulating molecular behavior. It generates samples of the possible states of molecular systems. To generate a sample efficiently, it is advantageous to avoid suggesting extremely high-energy states that would never become possible states. In this study, we propose a new sampling method for Monte Carlo molecular simulation, that is, a continuous normalizing molecular flow (CNMF) method, which can create various probabilistic distributions of molecular states from some initial distribution. The CNMF method generates samples by solving a first-order differential equation with two-body intermolecular interaction terms. We also develop specific probabilistic distributions using CNMF called inverse square flow, which yields distributions with zero probability density when molecule pairs are in close proximity, whereas probability densities are compressed uniformly from the initial distribution in all other cases. Using inverse square flow, we demonstrate that Monte Carlo molecular simulation is more efficient than the standard simulation. Although the increased computational costs of the CNMF method are non-negligible, this method is feasible for parallel computation and has the potential for expansion.

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Section: Resultsmentioning

confidence: 99%

Section: T H I S C O N T E N T Imentioning

confidence: 99%

Efficient Monte Carlo Sampling for Molecular Systems Using Continuous Normalizing Flow

Endo

Yuhara

Yasuoka

2022

J. Chem. Theory Comput.

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“…All the results were almost same as that of the SPME. The electrostatic potential profile ψ ( z ) is well known as one of the properties sensitive to the cutoff radius 84 , 90 , 92 , 100 – 103 , and thus should be calculated to evaluate the accuracy of the truncation methods. ψ ( z ) was calculated using the double integration of the Poisson equation: where z is the direction normal to the interface and ρ c is the charge density profile for the z -direction.…”

Section: Resultsmentioning

confidence: 99%

“…An extended IPS technique, that is, the linear-combination-based IPS (LIPS) was developed to improve the accuracy of the IPS for both homogeneous and heterogeneous systems 7 , 100 – 103 . The LIPS provides periodic reaction fields that can design pseudo pair potentials in the range of extended IPS theory.…”

Section: Introductionmentioning

confidence: 99%

A fast and accurate computational method for the linear-combination-based isotropic periodic sum

Takahashi

Nozawa

Yasuoka

2018

Sci Rep

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An isotropic periodic sum (IPS) is a powerful technique to reasonably calculate intermolecular interactions for wide range of molecular systems under periodic boundary conditions. A linear-combination-based IPS (LIPS) has been developed to attain computational accuracy close to an exact lattice sum, such as the Ewald sum. The algorithm of the original LIPS method has a high computational cost because it needs long-range interaction calculations in real space. This becomes a performance bottleneck for long-time molecular simulations. In this work, the combination of an LIPS and fast Fourier transform (FFT) was developed, and evaluated on homogeneous and heterogeneous molecular systems. This combinational approach of LIPS/FFT attained computational efficiency close to that of a smooth particle mesh Ewald while maintaining the same high accuracy as the original LIPS. We concluded that LIPS/FFT has great potential to extend the capability of IPS techniques for the fast and accurate computation of many types of molecular systems.

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“…The Journal of Chemical Physics ARTICLE scitation.org/journal/jcp to many interaction types 7,[17][18][19][20][21][22][23][24] and has been applied in many studies. [25][26][27][28] Even though IPS potentials can be solved analytically for many potential types, complicated mathematic work remains a burden for new interaction types. In addition, analytic solutions are often complicated in functional forms and are inconvenient to be implemented directly into simulation software.…”

Section: Introductionmentioning

confidence: 99%

The homogeneity condition: A simple way to derive isotropic periodic sum potentials for efficient calculation of long-range interactions in molecular simulation

Wu¹,

Brooks²

2019

The Journal of Chemical Physics

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Isotropic periodic sum (IPS) is a method to calculate long-range interactions based on the homogeneity of simulation systems. By using the isotropic periodic images of a local region to represent remote structures, long-range interactions become a function of the local conformation. This function is called the IPS potential, which folds long-ranged interactions into a short-ranged potential and can be calculated as efficiently as a cutoff method. Analytic solutions of IPS potentials have been solved for many interaction types. To further simplify the application of the IPS method, this work presents the homogeneity condition, which requires the sum of interaction energies for any particle to be independent of cutoff distances for a truly homogeneous system. Using the homogeneity condition, one can avoid the complicated mathematic work to solve analytic solutions and can instead use simple functions as IPS potentials. Example simulations are performed for model systems of a series of interaction types. Energies, volumes, and their fluctuations from these simulations demonstrate that simple IPS potentials obtained through the homogeneity condition can satisfactorily describe long-range interactions. The homogeneity condition makes the IPS method a convenient way to handle long-range interactions of any type.

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Critical test of isotropic periodic sum techniques with group-based cut-off schemes

Cited by 6 publications

References 61 publications

Efficient Monte Carlo Sampling for Molecular Systems Using Continuous Normalizing Flow

Efficient Monte Carlo Sampling for Molecular Systems Using Continuous Normalizing Flow

A fast and accurate computational method for the linear-combination-based isotropic periodic sum

The homogeneity condition: A simple way to derive isotropic periodic sum potentials for efficient calculation of long-range interactions in molecular simulation

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