We extend the recent formulation of the Ewald sum for electrostatics in a two-dimensionally periodic three-dimensional multi- atom layer or two-dimensional single-atom layer system with a rectangular periodic boundary...We extend the recent formulation of the Ewald sum for electrostatics in a two-dimensionally periodic three-dimensional multi- atom layer or two-dimensional single-atom layer system with a rectangular periodic boundary condition （J Chem Theory, Comput, 2014, 10： 534-542） to that with a parallelogrammic periodic boundary condition in general. Following the discussion of an efficient implementation of the formula, we suggest a simple setup of parameters using a relatively smaller screening factor and the associated larger real space cutoff distance to reach an optimized algorithm of an order N computational cost. The connection between the previous application of the Ewald sum to ionic crystal systems and the future application to mo- lecular self-assembly or disassembly systems on solid surfaces or at liquid-liquid interfaces ate illustrated to demonstrate the applicability of the present work to simulate the self-assembly process and to produce dynamical, structural and thermody- namic properties of experimental self-assembly systems of interest.展开更多
利用简单多项式基组拟合变化平缓的长程作用部分,并增加多个限定条件以提高优化势与库仑势的局部重合度,对Natoli优化法进行改进.在不增加计算复杂度的前提下,得到平均偏差明显降低的优化势;建议优化时划分r空间与k空间的准则取k c r c...利用简单多项式基组拟合变化平缓的长程作用部分,并增加多个限定条件以提高优化势与库仑势的局部重合度,对Natoli优化法进行改进.在不增加计算复杂度的前提下,得到平均偏差明显降低的优化势;建议优化时划分r空间与k空间的准则取k c r c≥15.在稠密液氢分子模拟中,优化法获得的能量及压力均小于Natoli法与Ewald法的结果.展开更多
Ewald summation method, based on Non-Uniform FFTs (ENUF) to compute the electrostatic interactions and forces, is implemented in two different particle simulation schemes to model molecular and soft matter, in classic...Ewald summation method, based on Non-Uniform FFTs (ENUF) to compute the electrostatic interactions and forces, is implemented in two different particle simulation schemes to model molecular and soft matter, in classical all-atom Molecular Dynamics and in Dissipative Particle Dynamics for coarse-grained particles. The method combines the traditional Ewald method with a non-uniform fast Fourier transform library (NFFT), making it highly efficient. It scales linearly with the number of particles as , while being both robust and accurate. It conserves both energy and the momentum to float point accuracy. As demonstrated here, it is straight- forward to implement the method in existing computer simulation codes to treat the electrostatic interactions either between point-charges or charge distributions. It should be an attractive alternative to mesh-based Ewald methods.展开更多
Modern computer simulations of biological systems often involve an explicit treatment of the complex interactions among a large number of molecules. While it is straightforward to compute the short-ranged Van der Waal...Modern computer simulations of biological systems often involve an explicit treatment of the complex interactions among a large number of molecules. While it is straightforward to compute the short-ranged Van der Waals interaction in classical molecular dynamics simulations, it has been a long-lasting issue to develop accurate methods for the longranged Coulomb interaction. In this short review, we discuss three types of methodologies for the accurate treatment of electrostatics in simulations of explicit molecules： truncation-type methods, Ewald-type methods, and mean-field-type methods. Throughout the discussion, we brief the formulations and developments of these methods, emphasize the intrinsic connections among the three types of methods, and focus on the existing problems which are often associated with the boundary conditions of electrostatics. This brief survey is summarized with a short perspective on future trends along the method developments and applications in the field of biological simulations.展开更多
Nature at the lab level in biology and chemistry can be described by the application of quantum mechanics.In many cases,a reasonable approximation to quantum mechanics is classical mechanics realized through Newton...Nature at the lab level in biology and chemistry can be described by the application of quantum mechanics.In many cases,a reasonable approximation to quantum mechanics is classical mechanics realized through Newton's equations of motion.Dr.Pedersen began his career using quantum mechanics to describe the properties of small molecular complexes that could serve as models for biochemical systems.To describe large molecular systems required a drop-back to classical means and this led surprisingly to a major improvement in the classical treatment of electrostatics for all molecules,not just biological molecules.Recent work has involved the application of quantum mechanics for the putative active sites of enzymes to gain greater insight into the key steps in enzyme catalysis.展开更多
基金supported by the National Natural Science Foundation of China(91127015,21103063(Z.H.))
文摘We extend the recent formulation of the Ewald sum for electrostatics in a two-dimensionally periodic three-dimensional multi- atom layer or two-dimensional single-atom layer system with a rectangular periodic boundary condition （J Chem Theory, Comput, 2014, 10： 534-542） to that with a parallelogrammic periodic boundary condition in general. Following the discussion of an efficient implementation of the formula, we suggest a simple setup of parameters using a relatively smaller screening factor and the associated larger real space cutoff distance to reach an optimized algorithm of an order N computational cost. The connection between the previous application of the Ewald sum to ionic crystal systems and the future application to mo- lecular self-assembly or disassembly systems on solid surfaces or at liquid-liquid interfaces ate illustrated to demonstrate the applicability of the present work to simulate the self-assembly process and to produce dynamical, structural and thermody- namic properties of experimental self-assembly systems of interest.
文摘利用简单多项式基组拟合变化平缓的长程作用部分,并增加多个限定条件以提高优化势与库仑势的局部重合度,对Natoli优化法进行改进.在不增加计算复杂度的前提下,得到平均偏差明显降低的优化势;建议优化时划分r空间与k空间的准则取k c r c≥15.在稠密液氢分子模拟中,优化法获得的能量及压力均小于Natoli法与Ewald法的结果.
文摘Ewald summation method, based on Non-Uniform FFTs (ENUF) to compute the electrostatic interactions and forces, is implemented in two different particle simulation schemes to model molecular and soft matter, in classical all-atom Molecular Dynamics and in Dissipative Particle Dynamics for coarse-grained particles. The method combines the traditional Ewald method with a non-uniform fast Fourier transform library (NFFT), making it highly efficient. It scales linearly with the number of particles as , while being both robust and accurate. It conserves both energy and the momentum to float point accuracy. As demonstrated here, it is straight- forward to implement the method in existing computer simulation codes to treat the electrostatic interactions either between point-charges or charge distributions. It should be an attractive alternative to mesh-based Ewald methods.
基金Project supported by the National Natural Science Foundation of China(Grant Nos.91127015 and 21522304)the Open Project from the State Key Laboratory of Theoretical Physicsthe Innovation Project from the State Key Laboratory of Supramolecular Structure and Materials
文摘Modern computer simulations of biological systems often involve an explicit treatment of the complex interactions among a large number of molecules. While it is straightforward to compute the short-ranged Van der Waals interaction in classical molecular dynamics simulations, it has been a long-lasting issue to develop accurate methods for the longranged Coulomb interaction. In this short review, we discuss three types of methodologies for the accurate treatment of electrostatics in simulations of explicit molecules： truncation-type methods, Ewald-type methods, and mean-field-type methods. Throughout the discussion, we brief the formulations and developments of these methods, emphasize the intrinsic connections among the three types of methods, and focus on the existing problems which are often associated with the boundary conditions of electrostatics. This brief survey is summarized with a short perspective on future trends along the method developments and applications in the field of biological simulations.
基金Supported by The National Institutes of Health (HL-006350)National Science Foundation (FRG DMR 0804549)
文摘Nature at the lab level in biology and chemistry can be described by the application of quantum mechanics.In many cases,a reasonable approximation to quantum mechanics is classical mechanics realized through Newton's equations of motion.Dr.Pedersen began his career using quantum mechanics to describe the properties of small molecular complexes that could serve as models for biochemical systems.To describe large molecular systems required a drop-back to classical means and this led surprisingly to a major improvement in the classical treatment of electrostatics for all molecules,not just biological molecules.Recent work has involved the application of quantum mechanics for the putative active sites of enzymes to gain greater insight into the key steps in enzyme catalysis.
