M.DynaMix – a scalable portable parallel MD simulation package for arbitrary molecular mixtures (original) (raw)
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MODYLAS: A highly parallelized general-purpose molecular dynamics simulation program
International Journal of Quantum Chemistry, 2014
Our new molecular dynamics (MD) simulation program, MODYLAS, is a general-purpose program appropriate for very large physical, chemical, and biological systems. It is equipped with most standard MD techniques. Long-range forces are evaluated rigorously by the fast multipole method (FMM) without using the fast Fourier transform (FFT). Several new methods have also been developed for extremely fine-grained parallelism of the MD calculation. The virtually buffering-free methods for communications and arithmetic operations, the minimal communication latency algorithm, and the parallel bucket-relay communication algorithm for the upper-level multipole moments in the FMM realize excellent scalability. The methods for blockwise arithmetic operations avoid data reload, attaining very small cache miss rates. Benchmark tests for MODYLAS using 65,536 nodes of the K-computer showed that the overall calculation time per MD step including communications is as short as about 5 ms for a 10 million-atom system; i.e., 35 ns of simulation time can be computed per day. The program enables investigations of large-scale real systems such as viruses, liposomes, assemblies of proteins and micelles, and polymers.
Introduction to Molecular Dynamics Simulation
In this chapter a summary is given of the key ingredients necessary to carry out a molecular dynamics simulation, with particular emphasis on macromolecular systems. We discuss the form of the intermolecular potential for molecules composed of atoms, and of non-spherical sub-units, giving examples of how to compute the forces and torques. We also describe some of the MD algorithms in current use. Finally, we briefly refer to the factors that influence the size of systems, and length of runs, that are needed to calculate statistical properties.
Introduction fo the molecular dynamic simulation
In this chapter a summary is given of the key ingredients necessary to carry out a molecular dynamics simulation, with particular emphasis on macromolecular systems. We discuss the form of the intermolecular potential for molecules composed of atoms, and of non-spherical sub-units, giving examples of how to compute the forces and torques. We also describe some of the MD algorithms in current use. Finally, we briefly refer to the factors that influence the size of systems, and length of runs, that are needed to calculate statistical properties.
Algorithms for Molecular Dynamics Simulations
2006
Methods for performing large-scale parallel Molecular Dynamics(MD) simulations are investigated. A perspective on the field of parallel md simulations is given. Hardware and software aspects are characterized and the interplay between the two is briefly discussed. A method for performing ab initio md is described; the method essentially recomputes the interaction potential at each time-step. It has been tested on a system of liquid water by comparing results with other simulation methods and experimental results. Different strategies for parallelization are explored. Furthermore, data-parallel methods for short-range and long-range interactions on massively parallel platforms are described and compared. Next, a method for treating electrostatic interactions in md simulations is developed. It combines the traditional Ewald summation technique with the nonuniform Fast Fourier transform-ENUF for short. The method scales as O(N log N), where N is the number of charges in the system. ENUF has a behavior very similar to Ewald summation and can be easily and efficiently implemented in existing simulation programs. Finally, an outlook is given and some directions for further developments are suggested.
MDLab: A molecular dynamics simulation prototyping environment
Journal of Computational Chemistry, 2009
Molecular dynamics (MD) simulation involves solving Newton's equations of motion for a system of atoms, by calculating forces and updating atomic positions and velocities over a timestep ∆t. Despite the large amount of computing power currently available, the timescale of MD simulations is limited by both the small timestep required for propagation, and the expensive algorithm for computing pairwise forces. These issues are currently addressed through the development of efficient simulation methods, some of which make acceptable approximations and as a result can afford larger timesteps. We present MDLab, a development environment for MD simulations built with Python which facilitates prototyping, testing, and debugging of these methods. MDLab provides constructs which allow the development of propagators, force calculators, and high level sampling protocols that run several instances of molecular dynamics. For computationally demanding sampling protocols which require testing on large biomolecules, MDL includes an interface to the OpenMM libraries of Friedrichs et al. which execute on graphical processing units (GPUs) and achieve considerable speedup over execution on the CPU. As an example of an interesting high level method developed in MDLab, we present a parallel implementation of the On-The-Fly String Method of Maragliano and Vanden-Eijnden. MDLab is available at http://mdlab.sourceforge.net.
ms2: A molecular simulation tool for thermodynamic properties
Computer Physics Communications, 2011
This work presents the molecular simulation program ms2 that is designed for the calculation of thermodynamic properties of bulk fluids in equilibrium consisting of small electro-neutral molecules. ms2 features the two main molecular simulation techniques, molecular dynamics (MD) and Monte-Carlo. It supports the calculation of vapor-liquid equilibria of pure fluids and multi-component mixtures described by rigid molecular models on the basis of the grand equilibrium method. Furthermore, it is capable of sampling various classical ensembles and yields numerous thermodynamic properties. To evaluate the chemical potential, Widom's test molecule method and gradual insertion are implemented. Transport properties are determined by equilibrium MD simulations following the Green-Kubo formalism. ms2 is designed to meet the requirements of academia and industry, particularly achieving short response times and straightforward handling. It is written in Fortran90 and optimized for a fast execution on a broad range of computer architectures, spanning from single processor PCs over PCclusters and vector computers to high-end parallel machines. The standard Message Passing Interface (MPI) is used for parallelization and ms2 is therefore easily portable onto a broad range of computing platforms. Auxiliary feature tools facilitate the interaction with the code and the interpretation of input and output files. The accuracy and reliability of ms2 has been shown for a large variety of fluids in preceding work.
Journal of Computational Chemistry, 1997
In this study, we present a new molecular dynamics program for simulation of complex molecular systems. The program, named ORAC, combines Ž . state-of-the-art molecular dynamics MD algorithms with flexibility in handling different types and sizes of molecules. ORAC is intended for simulations of molecular systems and is specifically designed to treat biomolecules efficiently and effectively in solution or in a crystalline environment. Among its unique Ž . features are: i implementation of reversible and symplectic multiple time step Ž . algorithms or r-RESPA, reversible reference system propagation algorithm specifically designed and tuned for biological systems with periodic boundary Ž . conditions; ii availability for simulations with multiple or single time steps of Ž . standard Ewald or smooth particle mesh Ewald SPME for computation of Ž . electrostatic interactions; and iii possibility of simulating molecular systems in a variety of thermodynamic ensembles. We believe that the combination of these algorithms makes ORAC more advanced than other MD programs using standard simulation algorithms.
Molecular dynamics simulations: advances and applications
Advances and Applications in Bioinformatics and Chemistry, 2015
Molecular dynamics simulations have evolved into a mature technique that can be used effectively to understand macromolecular structure-to-function relationships. Present simulation times are close to biologically relevant ones. Information gathered about the dynamic properties of macromolecules is rich enough to shift the usual paradigm of structural bioinformatics from studying single structures to analyze conformational ensembles. Here, we describe the foundations of molecular dynamics and the improvements made in the direction of getting such ensemble. Specific application of the technique to three main issues (allosteric regulation, docking, and structure refinement) is discussed.
Journal of Chemical Theory and Computation, 2013
Our new molecular dynamics (MD) simulation program, MODYLAS, is a general-purpose program appropriate for very large physical, chemical, and biological systems. It is equipped with most standard MD techniques. Long-range forces are evaluated rigorously by the fast multipole method (FMM) without using the fast Fourier transform (FFT). Several new methods have also been developed for extremely fine-grained parallelism of the MD calculation. The virtually buffering-free methods for communications and arithmetic operations, the minimal communication latency algorithm, and the parallel bucket-relay communication algorithm for the upper-level multipole moments in the FMM realize excellent scalability. The methods for blockwise arithmetic operations avoid data reload, attaining very small cache miss rates. Benchmark tests for MODYLAS using 65,536 nodes of the K-computer showed that the overall calculation time per MD step including communications is as short as about 5 ms for a 10 million-atom system; i.e., 35 ns of simulation time can be computed per day. The program enables investigations of large-scale real systems such as viruses, liposomes, assemblies of proteins and micelles, and polymers.