共查询到20条相似文献，搜索用时 15 毫秒
1.
《Journal of computational chemistry》2017,38(25):2193-2206
GENeralized‐Ensemble SImulation System (GENESIS) is a software package for molecular dynamics (MD) simulation of biological systems. It is designed to extend limitations in system size and accessible time scale by adopting highly parallelized schemes and enhanced conformational sampling algorithms. In this new version, GENESIS 1.1, new functions and advanced algorithms have been added. The all‐atom and coarse‐grained potential energy functions used in AMBER and GROMACS packages now become available in addition to CHARMM energy functions. The performance of MD simulations has been greatly improved by further optimization, multiple time‐step integration, and hybrid (CPU + GPU) computing. The string method and replica‐exchange umbrella sampling with flexible collective variable choice are used for finding the minimum free‐energy pathway and obtaining free‐energy profiles for conformational changes of a macromolecule. These new features increase the usefulness and power of GENESIS for modeling and simulation in biological research. © 2017 Wiley Periodicals, Inc. 相似文献
2.
We describe an algorithm for computing nonbonded interactions with cutoffs on a graphics processing unit. We have incorporated it into OpenMM, a library for performing molecular simulations on high‐performance computer architectures. We benchmark it on a variety of systems including boxes of water molecules, proteins in explicit solvent, a lipid bilayer, and proteins with implicit solvent. The results demonstrate that its performance scales linearly with the number of atoms over a wide range of system sizes, while being significantly faster than other published algorithms. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010 相似文献
3.
Ying Zhao Antonio De Nicola Toshihiro Kawakatsu Giuseppe Milano 《Journal of computational chemistry》2012,33(8):868-880
The parallel implementation of a recently developed hybrid scheme for molecular dynamics (MD) simulations (Milano and Kawakatsu, J Chem Phys 2009, 130, 214106) where self‐consistent field theory (SCF) and particle models are combined is described. Because of the peculiar formulation of the hybrid method, considering single particles interacting with density fields, the most computationally expensive part of the hybrid particle‐field MD simulation can be efficiently parallelized using a straightforward particle decomposition algorithm. Benchmarks of simulations, including comparisons of serial MD and MD‐SCF program profiles, serial MD‐SCF and parallel MD‐SCF program profiles, and parallel benchmarks compared with efficient MD program GROMACS 4.5.4 are tested and reported. The results of benchmarks indicate that the proposed parallelization scheme is very efficient and opens the way to molecular simulations of large scale systems with reasonable computational costs. © 2012 Wiley Periodicals, Inc. 相似文献
4.
Sergey Kazachenko Mark Giovinazzo Kyle Wm. Hall Natalie M. Cann 《Journal of computational chemistry》2015,36(24):1787-1804
A custom code for molecular dynamics simulations has been designed to run on CUDA‐enabled NVIDIA graphics processing units (GPUs). The double‐precision code simulates multicomponent fluids, with intramolecular and intermolecular forces, coarse‐grained and atomistic models, holonomic constraints, Nosé–Hoover thermostats, and the generation of distribution functions. Algorithms to compute Lennard‐Jones and Gay‐Berne interactions, and the electrostatic force using Ewald summations, are discussed. A neighbor list is introduced to improve scaling with respect to system size. Three test systems are examined: SPC/E water; an n‐hexane/2‐propanol mixture; and a liquid crystal mesogen, 2‐(4‐butyloxyphenyl)‐5‐octyloxypyrimidine. Code performance is analyzed for each system. With one GPU, a 33–119 fold increase in performance is achieved compared with the serial code while the use of two GPUs leads to a 69–287 fold improvement and three GPUs yield a 101–377 fold speedup. © 2015 Wiley Periodicals, Inc. 相似文献
5.
Francesco Aquilante Jochen Autschbach Rebecca K. Carlson Liviu F. Chibotaru Mickaël G. Delcey Luca De Vico Ignacio Fdez. Galván Nicolas Ferré Luis Manuel Frutos Laura Gagliardi Marco Garavelli Angelo Giussani Chad E. Hoyer Giovanni Li Manni Hans Lischka Dongxia Ma Per Åke Malmqvist Thomas Müller Artur Nenov Massimo Olivucci Thomas Bondo Pedersen Daoling Peng Felix Plasser Ben Pritchard Markus Reiher Ivan Rivalta Igor Schapiro Javier Segarra‐Martí Michael Stenrup Donald G. Truhlar Liviu Ungur Alessio Valentini Steven Vancoillie Valera Veryazov Victor P. Vysotskiy Oliver Weingart Felipe Zapata Roland Lindh 《Journal of computational chemistry》2016,37(5):506-541
6.
Stone JE Phillips JC Freddolino PL Hardy DJ Trabuco LG Schulten K 《Journal of computational chemistry》2007,28(16):2618-2640
Molecular mechanics simulations offer a computational approach to study the behavior of biomolecules at atomic detail, but such simulations are limited in size and timescale by the available computing resources. State-of-the-art graphics processing units (GPUs) can perform over 500 billion arithmetic operations per second, a tremendous computational resource that can now be utilized for general purpose computing as a result of recent advances in GPU hardware and software architecture. In this article, an overview of recent advances in programmable GPUs is presented, with an emphasis on their application to molecular mechanics simulations and the programming techniques required to obtain optimal performance in these cases. We demonstrate the use of GPUs for the calculation of long-range electrostatics and nonbonded forces for molecular dynamics simulations, where GPU-based calculations are typically 10-100 times faster than heavily optimized CPU-based implementations. The application of GPU acceleration to biomolecular simulation is also demonstrated through the use of GPU-accelerated Coulomb-based ion placement and calculation of time-averaged potentials from molecular dynamics trajectories. A novel approximation to Coulomb potential calculation, the multilevel summation method, is introduced and compared with direct Coulomb summation. In light of the performance obtained for this set of calculations, future applications of graphics processors to molecular dynamics simulations are discussed. 相似文献
7.
Yasuda K 《Journal of computational chemistry》2008,29(3):334-342
We propose the algorithm to evaluate the Coulomb potential in the ab initio density functional calculation on the graphics processor unit (GPU). The numerical accuracy required for the algorithm is investigated in detail. It is shown that GPU, which supports only the single-precision floating number natively, can take part in the major computational tasks. Because of the limited size of the working memory, the Gauss-Rys quadrature to evaluate the electron repulsion integrals (ERIs) is investigated in detail. The error analysis of the quadrature is performed. New interpolation formula of the roots and weights is presented, which is suitable for the processor of the single-instruction multiple-data type. It is proposed to calculate only small ERIs on GPU. ERIs can be classified efficiently with the upper-bound formula. The algorithm is implemented on NVIDIA GeForce 8800 GTX and the Gaussian 03 program suite. It is applied to the test molecules Taxol and Valinomycin. The total energies calculated are essentially the same as the reference ones. The preliminary results show the considerable speedup over the commodity microprocessor. 相似文献
8.
Nathan Schmid Mathias Bötschi Wilfred F. Van Gunsteren 《Journal of computational chemistry》2010,31(8):1636-1643
During the past few years, graphics processing units (GPUs) have become extremely popular in the high performance computing community. In this study, we present an implementation of an acceleration engine for the solvent–solvent interaction evaluation of molecular dynamics simulations. By careful optimization of the algorithm speed‐ups up to a factor of 54 (single‐precision GPU vs. double‐precision CPU) could be achieved. The accuracy of the single‐precision GPU implementation is carefully investigated and does not influence structural, thermodynamic, and dynamic quantities. Therefore, the implementation enables users of the GROMOS software for biomolecular simulation to run the solvent–solvent interaction evaluation on a GPU, and thus, to speed‐up their simulations by a factor 6–9. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010 相似文献
9.
Lennart Heinzerling Robert Klein Matthias Rarey 《Journal of computational chemistry》2012,33(32):2554-2565
Usually based on molecular mechanics force fields, the post-optimization of ligand poses is typically the most time-consuming step in protein–ligand docking procedures. In return, it bears the potential to overcome the limitations of discretized conformation models. Because of the parallel nature of the problem, recent graphics processing units (GPUs) can be applied to address this dilemma. We present a novel algorithmic approach for parallelizing and thus massively speeding up protein–ligand complex optimizations with GPUs. The method, customized to pose-optimization, performs at least 100 times faster than widely used CPU-based optimization tools. An improvement in Root-Mean-Square Distance (RMSD) compared to the original docking pose of up to 42% can be achieved. © 2012 Wiley Periodicals, Inc. 相似文献
10.
We have developed a new hybrid (MPI+OpenMP) parallelization scheme for molecular dynamics (MD) simulations by combining a cell‐wise version of the midpoint method with pair‐wise Verlet lists. In this scheme, which we call the midpoint cell method, simulation space is divided into subdomains, each of which is assigned to a MPI processor. Each subdomain is further divided into small cells. The interaction between two particles existing in different cells is computed in the subdomain containing the midpoint cell of the two cells where the particles reside. In each MPI processor, cell pairs are distributed over OpenMP threads for shared memory parallelization. The midpoint cell method keeps the advantages of the original midpoint method, while filtering out unnecessary calculations of midpoint checking for all the particle pairs by single midpoint cell determination prior to MD simulations. Distributing cell pairs over OpenMP threads allows for more efficient shared memory parallelization compared with distributing atom indices over threads. Furthermore, cell grouping of particle data makes better memory access, reducing the number of cache misses. The parallel performance of the midpoint cell method on the K computer showed scalability up to 512 and 32,768 cores for systems of 20,000 and 1 million atoms, respectively. One MD time step for long‐range interactions could be calculated within 4.5 ms even for a 1 million atoms system with particle‐mesh Ewald electrostatics. © 2014 Wiley Periodicals, Inc. 相似文献
11.
Jinzu Weng Xi Chen Zhen Yao Lorenz T. Biegler 《Macromolecular theory and simulations》2015,24(5):521-536
12.
The computation of electron repulsion integrals (ERIs) is the most time‐consuming process in the density functional calculation using Gaussian basis set. Many temporal ERIs are calculated, and most are stored on slower storage, such as cache or memory, because of the shortage of registers, which are the fastest storage in a central processing unit (CPU). Moreover, the heavy register usage makes it difficult to launch many concurrent threads on a graphics processing unit (GPU) to hide latency. Hence, we propose to optimize the calculation order of one‐center ERIs to minimize the number of registers used, and to calculate each ERI with three or six co‐operating threads. The performance of this method is measured on a recent CPU and a GPU. The proposed approach is found to be efficient for high angular basis functions with a GPU. When combined with a recent GPU, it accelerates the computation almost 4‐fold. © 2014 Wiley Periodicals, Inc. 相似文献
13.
《Journal of computational chemistry》2018,39(22):1764-1778
We develop novel parallel algorithms that allow molecular dynamics simulations in which byproduct molecules are created and removed because of the chemical reactions during the molecular dynamics simulation. To prevent large increases in the potential energy, we introduce the byproduct molecules smoothly by changing the non‐bonded interactions gradually. To simulate complete equilibrium reactions, we allow the byproduct molecules attack and destroy created bonds. Modeling of such reactions are, for instance, important to study the pore formation due to the presence of e.g. water molecules or development of polymer morphology during the process of splitting off byproduct molecules. Another concept that could be studied is the degradation of polymeric materials, a very important topic in a recycling of polymer waste. We illustrate the method by simulating the polymerization of polyethylene terephthalate (PET) at the coarse‐grained level as an example of a polycondensation reaction with water as a byproduct. The algorithms are implemented in a publicly available software package and are easily accessible using a domain‐specific language that describes chemical reactions in an input configuration file. © 2018 Wiley Periodicals, Inc. 相似文献
14.
Yutaka Maruyama;Norio Yoshida; 《Journal of computational chemistry》2024,45(17):1470-1482
Solvent plays an essential role in a variety of chemical, physical, and biological processes that occur in the solution phase. The reference interaction site model (RISM) and its three-dimensional extension (3D-RISM) serve as powerful computational tools for modeling solvation effects in chemical reactions, biological functions, and structure formations. We present the RISM integrated calculator (RISMiCal) program package, which is based on RISM and 3D-RISM theories with fast GPU code. RISMiCal has been developed as an integrated RISM/3D-RISM program that has interfaces with external programs such as Gaussian16, GAMESS, and Tinker. Fast 3D-RISM programs for single- and multi-GPU codes written in CUDA would enhance the availability of these hybrid methods because they require the performance of many computationally expensive 3D-RISM calculations. We expect that our package can be widely applied for chemical and biological processes in solvent. The RISMiCal package is available at https://rismical-dev.github.io. 相似文献
15.
The distributed diagonal force decomposition method for parallelizing molecular dynamics simulations
Parallelization is an effective way to reduce the computational time needed for molecular dynamics simulations. We describe a new parallelization method, the distributed-diagonal force decomposition method, with which we extend and improve the existing force decomposition methods. Our new method requires less data communication during molecular dynamics simulations than replicated data and current force decomposition methods, increasing the parallel efficiency. It also dynamically load-balances the processors' computational load throughout the simulation. The method is readily implemented in existing molecular dynamics codes and it has been incorporated into the CHARMM program, allowing its immediate use in conjunction with the many molecular dynamics simulation techniques that are already present in the program. We also present the design of the Force Decomposition Machine, a cluster of personal computers and networks that is tailored to running molecular dynamics simulations using the distributed diagonal force decomposition method. The design is expandable and provides various degrees of fault resilience. This approach is easily adaptable to computers with Graphics Processing Units because it is independent of the processor type being used. 相似文献
16.
M. Ángeles Pérez García 《Journal of mathematical chemistry》2006,40(1):63-69
In this work we present a calculation of the hamiltonian variables solving the molecular dynamics equations of motion for a system of nuclear matter kept at fixed temperature by using the Nosé-Hoover Thermostat and interacting via a semiclassical potential depending on both positions and momenta. 相似文献
17.
We introduce a complete implementation of viscoelastic model for numerical simulations of the phase separation kinetics in dynamic asymmetry systems such as polymer blends and polymer solutions on a graphics processing unit (GPU) by CUDA language and discuss algorithms and optimizations in details. From studies of a polymer solution, we show that the GPU-based implementation can predict correctly the accepted results and provide about 190 times speedup over a single central processing unit (CPU). Further accuracy analysis demonstrates that both the single and the double precision calculations on the GPU are sufficient to produce high-quality results in numerical simulations of viscoelastic model. Therefore, the GPU-based viscoelastic model is very promising for studying many phase separation processes of experimental and theoretical interests that often take place on the large length and time scales and are not easily addressed by a conventional implementation running on a single CPU. 相似文献
18.
Adam Górecki Marcin Szypowski Maciej Długosz Joanna Trylska 《Journal of computational chemistry》2009,30(14):2364-2373
We developed a software package (RedMD) to perform molecular dynamics simulations and normal mode analysis of reduced models of proteins, nucleic acids, and their complexes. With RedMD one can perform molecular dynamics simulations in a microcanonical ensemble, with Berendsen and Langevin thermostats, and with Brownian dynamics. We provide force field and topology generators which are based on the one‐bead per residue/nucleotide elastic network model and its extensions. The user can change the force field parameters with the command line options that are passed to generators. Also, the generators can be modified, for example, to add new potential energy functions. Normal mode analysis tool is available for elastic or anisotropic network models. The program is written in C and C++ languages and the structure/topology of a molecule is based on an XML format. OpenMP technology for shared‐memory architectures was used for code parallelization. The code is distributed under GNU public licence and available at http://bionano.icm.edu.pl/software/ . © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009 相似文献
19.
Ganesan N Bauer BA Lucas TR Patel S Taufer M 《Journal of computational chemistry》2011,32(14):2958-2973
We present results of molecular dynamics simulations of fully hydrated DMPC bilayers performed on graphics processing units (GPUs) using current state-of-the-art non-polarizable force fields and a local GPU-enabled molecular dynamics code named FEN ZI. We treat the conditionally convergent electrostatic interaction energy exactly using the particle mesh Ewald method (PME) for solution of Poisson's Equation for the electrostatic potential under periodic boundary conditions. We discuss elements of our implementation of the PME algorithm on GPUs as well as pertinent performance issues. We proceed to show results of simulations of extended lipid bilayer systems using our program, FEN ZI. We performed simulations of DMPC bilayer systems consisting of 17,004, 68,484, and 273,936 atoms in explicit solvent. We present bilayer structural properties (atomic number densities, electron density profiles), deuterium order parameters (S(CD)), electrostatic properties (dipole potential, water dipole moments), and orientational properties of water. Predicted properties demonstrate excellent agreement with experiment and previous all-atom molecular dynamics simulations. We observe no statistically significant differences in calculated structural or electrostatic properties for different system sizes, suggesting the small bilayer simulations (less than 100 lipid molecules) provide equivalent representation of structural and electrostatic properties associated with significantly larger systems (over 1000 lipid molecules). We stress that the three system size representations will have differences in other properties such as surface capillary wave dynamics or surface tension related effects that are not probed in the current study. The latter properties are inherently dependent on system size. This contribution suggests the suitability of applying emerging GPU technologies to studies of an important class of biological environments, that of lipid bilayers and their associated integral membrane proteins. We envision that this technology will push the boundaries of fully atomic-resolution modeling of these biological systems, thus enabling unprecedented exploration of meso-scale phenomena (mechanisms, kinetics, energetics) with atomic detail at commodity hardware prices. 相似文献
20.
A new algorithm is proposed for approximation to the molecular surface. It starts with a triangular mesh built on an ellipsoid embracing the whole molecular surface. The triangular mesh is obtained from an icosahedron subdivision sphere with highly uniform vertex distribution, and the embracing surface is deflated stepwise to the best adherence of its triangles onto the surface of the molecule. The deflating direction of each vertex of a triangle is defined by the vector normal at this point to the previous deflated embracing surface. Our results show that the speed of the triangulation embracing ellipsoid method and the quality of the surface obtained by the method are faster and better than the method that starts with a quadrilateral mesh built from meridian and parallel representations on an embracing sphere to get the molecular surface. Furthermore, the surface obtained by the method can be used directly to approximate the molecular surface by spherical harmonic expansions. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 1805–1815, 1998 相似文献