LINCS: A linear constraint solver for molecular simulations

The European Physical Journal Special Topics, 2011

Computational Methods for …, 2002

This article describes a collection of model problems for aiding numerical analysts, code developers and others in the design of computational methods for molecular dynamics (MD) simulation. Common types of calculations and desirable features of algorithms are surveyed, and these are used to guide selection of representative models. By including essential features of certain classes of molecular systems, but otherwise limiting the physical and quantitative details, it is hoped that the test set can help to facilitate cross-disciplinary algorithm and code development e orts.

2010

The most important factor for quantitative results in molecular dynamics simulation are well developed force fields and models. In the present work, the development of new models and the usage of force fields from the literature in large systems are presented. Both tasks lead to time consuming simulations that require massively parallel high performance computing. In the present work, new

1998

Journal of Computational Chemistry, 1995

Current macromolecular energy minimization algorithms become inefficient and prone to failure when bond length constraints are imposed. They are required to relieve steric stresses in biomolecules prior to a molecular dynamics simulation. Unfortunately, the latter often require constraints, leading to difficulties in initiating trajectories from unconstrained energy minima. This difficulty was overcome by requiring that the components of the energy gradient vanish along the constrained bonds. The modified energy minimization algorithm converges to a lower energy in a fewer number of iterations and is more robust than current implementations. The method has been successfully applied to the Dickerson DNA dodecamer, CGCGAA'ITCGCG. 0 1995 by John Wiley & Sons, Inc. techniques' are routinely used in X-ray diffraction studies of proteins and DNA to adjust bond lengths, bond angles, etc. so that they conform to known stereochemical values. They have been used extensively in the parameterization of molecular mechanics force fields's3 and in molecular dynambiomolecules, in which the stresses in the molecule lar structure and function. Gradient minimization ics (MD) and Monte Carlo (MC) studies of generally must be prior to the commencement of the simulation^^,^ and in which, for large

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.

Bioinformatics, 2013

Motivation: Molecular simulation has historically been a lowthroughput technique, but faster computers and increasing amounts of genomic and structural data are changing this by enabling large-scale automated simulation of, for instance, many conformers or mutants of biomolecules with or without a range of ligands. At the same time, advances in performance and scaling now make it possible to model complex biomolecular interaction and function in a manner directly testable by experiment. These applications share a need for fast and efficient software that can be deployed on massive scale in clusters, web servers, distributed computing or cloud resources.

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.

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.

Advances in Engineering Software, 1998

In this paper, a novel algorithm for solution of the constrained equations of motion with application to simulation of the molecular dynamics systems is presented. The algorithm enables the solution of equations of motion with an internal coordinates model wherein the high-frequency oscillations are frozen by explicit inclusion of hard constraints in the system as well as by clustering of atoms and, thus, allowing a much larger time step in the integration. For a molecular system with N clusters, the algorithm achieves the optimal sequential complexity of O(N). However, the main advantage of this new algorithm is its efficiency for massively parallel computation. In fact, this is the first known algorithm that achieves a both time-and processor-optimal parallel solution for the constrained equations of motion, i.e. an optimal computation time of O(logN) by using an optimal number of O(N) processors. In addition to its theoretical significance, this algorithm is also very efficient for practical implementation on the coarse grain MIMD parallel architectures owing to its highly decoupled computational structure. ᭧