The Experts below are selected from a list of 7101 Experts worldwide ranked by ideXlab platform
Ikuo Fukuda - One of the best experts on this subject based on the ideXlab platform.
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performance evaluation of the zero multipole summation method in modern molecular dynamics software
Journal of Computational Chemistry, 2018Co-Authors: Shun Sakuraba, Ikuo FukudaAbstract:The zero-multiple summation method (ZMM) is a Cutoff-based method for calculating electrostatic interactions in molecular dynamics simulations, utilizing an electrostatic neutralization principle as a physical basis. Since the accuracies of the ZMM have been revealed to be sufficient in previous studies, it is highly desirable to clarify its practical performance. In this paper, the performance of the ZMM is compared with that of the smooth particle mesh Ewald method (SPME), where the both methods are implemented in molecular dynamics software package GROMACS. Extensive performance comparisons against a highly optimized, parameter-tuned SPME implementation are performed for various-sized water systems and two protein-water systems. We analyze in detail the dependence of the performance on the potential parameters and the number of CPU cores. Even though the ZMM uses a larger Cutoff Distance than the SPME does, the performance of the ZMM is comparable to or better than that of the SPME. This is because the ZMM does not require a time-consuming electrostatic convolution and because the ZMM gains short neighbor-list Distances due to the smooth damping feature of the pairwise potential function near the Cutoff length. We found, in particular, that the ZMM with quadrupole or octupole cancellation and no damping factor is an excellent candidate for the fast calculation of electrostatic interactions. © 2018 Wiley Periodicals, Inc.
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performance evaluation of the zero multipole summation method in modern molecular dynamics software
arXiv: Computational Physics, 2017Co-Authors: Shun Sakuraba, Ikuo FukudaAbstract:We evaluate the practical performance of the zero-multiple summation method (ZMM), a method for approximately calculating electrostatic interactions in molecular dynamics simulations. The performance of the ZMM is compared with that of the smooth particle mesh Ewald method (SPME). Even though the ZMM uses a larger Cutoff Distance than the SPME does, the performance of the ZMM is found to be comparable to or better than that of the SPME. In particular, the ZMM with quadrupole or octupole cancellation and no damping factor is an excellent candidate for the fast calculation of electrostatic potentials.
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simple and accurate scheme to compute electrostatic interaction zero dipole summation technique for molecular system and application to bulk water
Journal of Chemical Physics, 2012Co-Authors: Ikuo Fukuda, Narutoshi Kamiya, Yasushige Yonezawa, Haruki NakamuraAbstract:The zero-dipole summation method was extended to general molecular systems, and then applied to molecular dynamics simulations of an isotropic water system. In our previous paper [I. Fukuda, Y. Yonezawa, and H. Nakamura, J. Chem. Phys. 134, 164107 (2011)], for evaluating the electrostatic energy of a classical particle system, we proposed the zero-dipole summation method, which conceptually prevents the nonzero-charge and nonzero-dipole states artificially generated by a simple Cutoff truncation. Here, we consider the application of this scheme to molecular systems, as well as some fundamental aspects of general Cutoff truncation protocols. Introducing an idea to harmonize the bonding interactions and the electrostatic interactions in the scheme, we develop a specific algorithm. As in the previous study, the resulting energy formula is represented by a simple pairwise function sum, enabling facile applications to high-performance computation. The accuracy of the electrostatic energies calculated by the zero-dipole summation method with the atom-based Cutoff was numerically investigated, by comparison with those generated by the Ewald method. We obtained an electrostatic energy error of less than 0.01% at a Cutoff length longer than 13 A for a TIP3P isotropic water system, and the errors were quite small, as compared to those obtained by conventional truncation methods. The static property and the stability in an MD simulation were also satisfactory. In addition, the dielectric constants and the Distance-dependent Kirkwood factors were measured, and their coincidences with those calculated by the particle mesh Ewald method were confirmed, although such coincidences are not easily attained by truncation methods. We found that the zero damping-factor gave the best results in a practical Cutoff Distance region. In fact, in contrast to the zero-charge scheme, the damping effect was insensitive in the zero-charge and zero-dipole scheme, in the molecular system we treated. We discussed the origin of this difference between the two schemes and the dependence of this fact on the physical system. The use of the zero damping-factor will enhance the efficiency of practical computations, since the complementary error function is not employed. In addition, utilizing the zero damping-factor provides freedom from the parameter choice, which is not trivial in the zero-charge scheme, and eliminates the error function term, which corresponds to the time-consuming Fourier part under the periodic boundary conditions.
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molecular dynamics scheme for precise estimation of electrostatic interaction via zero dipole summation principle
Journal of Chemical Physics, 2011Co-Authors: Ikuo Fukuda, Yasushige Yonezawa, Haruki NakamuraAbstract:We propose a novel idea, zero-dipole summation, for evaluating the electrostatic energy of a classical particle system, and have composed an algorithm for effectively utilizing the idea for molecular dynamics. It conceptually prevents the nonzero-charge and nonzero-dipole states artificially generated by a simple Cutoff truncation. The resulting energy formula is nevertheless represented by a simple pairwise function sum, which enables facile application to high-performance computation. By following a heuristic approach to derive the current electrostatic energy formula, we developed an axiomatic approach to construct the method consistently. Explorations of the theoretical details of our method revealed the structure of the generated error, and we analyzed it by comparisons with other methods. A numerical simulation using liquid sodium chloride confirmed that the current method with a small damping factor yielded sufficient accuracy with a practical Cutoff Distance region. The current energy function also conducts stable numerical integration in a liquid MD simulation. Our method is an extension of the charge neutralized summation developed by Wolf et al. [J. Chem. Phys. 110, 8254 (1999)]. Furthermore, we found that the current method becomes a generalization of the preaveraged potential method proposed by Yakub and Ronchi [J. Chem. Phys. 119, 11556 (2003)], which is based on a viewpoint different from the neutrality. The current study presents these relationships and suggests possibilities for their further applications.
Liu Yaohui - One of the best experts on this subject based on the ideXlab platform.
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adaptive density peak clustering based on k nearest neighbors with aggregating strategy
Knowledge Based Systems, 2017Co-Authors: Liu Yaohui, Ma Zhengming, Yu FangAbstract:Abstract Recently a density peaks based clustering algorithm (dubbed as DPC) was proposed to group data by setting up a decision graph and finding out cluster centers from the graph fast. It is simple but efficient since it is noniterative and needs few parameters. However, the improper selection of its parameter Cutoff Distance dc will lead to the wrong selection of initial cluster centers, but the DPC cannot correct it in the subsequent assignment process. Furthermore, in some cases, even the proper value of dc was set, initial cluster centers are still difficult to be selected from the decision graph. To overcome these defects, an adaptive clustering algorithm (named as ADPC-KNN) is proposed in this paper. We introduce the idea of K-nearest neighbors to compute the global parameter dc and the local density ρi of each point, apply a new approach to select initial cluster centers automatically, and finally aggregate clusters if they are density reachable. The ADPC-KNN requires only one parameter and the clustering is automatic. Experiments on synthetic and real-world data show that the proposed clustering algorithm can often outperform DBSCAN, DPC, K-Means++, Expectation Maximization (EM) and single-link.
Linfu Sun - One of the best experts on this subject based on the ideXlab platform.
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effective density peaks clustering algorithm based on the layered k nearest neighbors and subcluster merging
IEEE Access, 2020Co-Authors: Chunhua Ren, Linfu SunAbstract:Density peaks clustering (DPC) algorithm is a novel density-based clustering algorithm, which is simple and efficient, is not necessary to specify the number of clusters in advance, and can find any nonspherical class clusters. However, DPC relies heavily on the calculation methods of the Cutoff Distance threshold and local density and cannot analyze complex manifold data, especially datasets with uneven density distribution and multiple peaks in the same cluster. To solve these problems, we propose an improved density peaks clustering algorithm based on the layered k-nearest neighbors and subcluster merging (LKSM_DPC). First, we redefine the local density calculation method using the layered k-nearest neighbors. To adapt to datasets with different densities, the k-nearest neighbors are divided into multiple layers. Second, for the multiple peaks in the same cluster problem, we design a new mechanism to calculate the similarity of subclusters based on the idea of shared neighbors and Newton's law of gravitation, and a subcluster merging strategy is proposed. To prove the effectiveness of our algorithm, we compare the LKSM_DPC with K-means, DBSCAN, DPC, and DPC derivatives for 24 datasets. A large number of experiments demonstrate that our algorithm can often outperform other algorithms.
Haruki Nakamura - One of the best experts on this subject based on the ideXlab platform.
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simple and accurate scheme to compute electrostatic interaction zero dipole summation technique for molecular system and application to bulk water
Journal of Chemical Physics, 2012Co-Authors: Ikuo Fukuda, Narutoshi Kamiya, Yasushige Yonezawa, Haruki NakamuraAbstract:The zero-dipole summation method was extended to general molecular systems, and then applied to molecular dynamics simulations of an isotropic water system. In our previous paper [I. Fukuda, Y. Yonezawa, and H. Nakamura, J. Chem. Phys. 134, 164107 (2011)], for evaluating the electrostatic energy of a classical particle system, we proposed the zero-dipole summation method, which conceptually prevents the nonzero-charge and nonzero-dipole states artificially generated by a simple Cutoff truncation. Here, we consider the application of this scheme to molecular systems, as well as some fundamental aspects of general Cutoff truncation protocols. Introducing an idea to harmonize the bonding interactions and the electrostatic interactions in the scheme, we develop a specific algorithm. As in the previous study, the resulting energy formula is represented by a simple pairwise function sum, enabling facile applications to high-performance computation. The accuracy of the electrostatic energies calculated by the zero-dipole summation method with the atom-based Cutoff was numerically investigated, by comparison with those generated by the Ewald method. We obtained an electrostatic energy error of less than 0.01% at a Cutoff length longer than 13 A for a TIP3P isotropic water system, and the errors were quite small, as compared to those obtained by conventional truncation methods. The static property and the stability in an MD simulation were also satisfactory. In addition, the dielectric constants and the Distance-dependent Kirkwood factors were measured, and their coincidences with those calculated by the particle mesh Ewald method were confirmed, although such coincidences are not easily attained by truncation methods. We found that the zero damping-factor gave the best results in a practical Cutoff Distance region. In fact, in contrast to the zero-charge scheme, the damping effect was insensitive in the zero-charge and zero-dipole scheme, in the molecular system we treated. We discussed the origin of this difference between the two schemes and the dependence of this fact on the physical system. The use of the zero damping-factor will enhance the efficiency of practical computations, since the complementary error function is not employed. In addition, utilizing the zero damping-factor provides freedom from the parameter choice, which is not trivial in the zero-charge scheme, and eliminates the error function term, which corresponds to the time-consuming Fourier part under the periodic boundary conditions.
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molecular dynamics scheme for precise estimation of electrostatic interaction via zero dipole summation principle
Journal of Chemical Physics, 2011Co-Authors: Ikuo Fukuda, Yasushige Yonezawa, Haruki NakamuraAbstract:We propose a novel idea, zero-dipole summation, for evaluating the electrostatic energy of a classical particle system, and have composed an algorithm for effectively utilizing the idea for molecular dynamics. It conceptually prevents the nonzero-charge and nonzero-dipole states artificially generated by a simple Cutoff truncation. The resulting energy formula is nevertheless represented by a simple pairwise function sum, which enables facile application to high-performance computation. By following a heuristic approach to derive the current electrostatic energy formula, we developed an axiomatic approach to construct the method consistently. Explorations of the theoretical details of our method revealed the structure of the generated error, and we analyzed it by comparisons with other methods. A numerical simulation using liquid sodium chloride confirmed that the current method with a small damping factor yielded sufficient accuracy with a practical Cutoff Distance region. The current energy function also conducts stable numerical integration in a liquid MD simulation. Our method is an extension of the charge neutralized summation developed by Wolf et al. [J. Chem. Phys. 110, 8254 (1999)]. Furthermore, we found that the current method becomes a generalization of the preaveraged potential method proposed by Yakub and Ronchi [J. Chem. Phys. 119, 11556 (2003)], which is based on a viewpoint different from the neutrality. The current study presents these relationships and suggests possibilities for their further applications.
Yu Fang - One of the best experts on this subject based on the ideXlab platform.
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adaptive density peak clustering based on k nearest neighbors with aggregating strategy
Knowledge Based Systems, 2017Co-Authors: Liu Yaohui, Ma Zhengming, Yu FangAbstract:Abstract Recently a density peaks based clustering algorithm (dubbed as DPC) was proposed to group data by setting up a decision graph and finding out cluster centers from the graph fast. It is simple but efficient since it is noniterative and needs few parameters. However, the improper selection of its parameter Cutoff Distance dc will lead to the wrong selection of initial cluster centers, but the DPC cannot correct it in the subsequent assignment process. Furthermore, in some cases, even the proper value of dc was set, initial cluster centers are still difficult to be selected from the decision graph. To overcome these defects, an adaptive clustering algorithm (named as ADPC-KNN) is proposed in this paper. We introduce the idea of K-nearest neighbors to compute the global parameter dc and the local density ρi of each point, apply a new approach to select initial cluster centers automatically, and finally aggregate clusters if they are density reachable. The ADPC-KNN requires only one parameter and the clustering is automatic. Experiments on synthetic and real-world data show that the proposed clustering algorithm can often outperform DBSCAN, DPC, K-Means++, Expectation Maximization (EM) and single-link.
