Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

Fast parallel algorithms for short-range molecular dynamics

抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

In this article, we present a new LINear Constraint Solver (LINCS) for molecular simulations with bond constraints. The algorithm is inherently stable, as the constraints themselves are reset instead of derivatives of the constraints, thereby eliminating drift. Although the derivation of the algorithm is presented in terms of matrices, no matrix matrix multiplications are needed and only the nonzero matrix elements have to be stored, making the method useful for very large molecules. At the same accuracy, the LINCS algorithm is three to four times faster than the SHAKE algorithm. Parallelization of the algorithm is straightforward. (C) 1997 John Wiley & Sons, Inc.

LINCS : A linear constraint solver for molecular simulations

N G van Kampen 1981 Amsterdam: North-Holland xiv + 419 pp price Dfl 180 This is a book which, at a lower price, could be expected to become an essential part of the library of every physical scientist concerned with problems involving fluctuations and stochastic processes, as well as those who just enjoy a beautifully written book. It provides an extensive graduate-level introduction which is clear, cautious, interesting and readable.

https://iopscience.iop.org/article/10.1088/0031-9112/34/4/040/pdf

Stochastic Processes in Physics and Chemistry

http://experimentationlab.berkeley.edu/sites/default/files/AFMImages/butt_AFM.pdf

Force measurements with the atomic force microscope: Technique, interpretation and applications

An analytic theory for the structure and thermodynamics of two-component mixtures of patchy and spherical colloids is developed. The theory is based on an analytical solution of the multidensity Ornstein-Zernike equation supplemented by the associative Percus-Yevick closure relations. We derive closed-form analytic expressions for the partial structure factors and thermodynamic properties using the energy route for the model with arbitrary number of patches and any hard-sphere size ratio of the particles. To assess the accuracy of the theoretical predictions we compare them against existing and newly generated set of computer simulation data. In our numerical calculations we consider the model with equal hard-sphere sizes and one patch. Very good agreement between results of the theory and simulation for the pair correlation functions, excess internal energy and pressure is observed for almost all values of the system density, temperature and composition studied. Only in the region of low concentrations of spherical colloids the theoretical results become less accurate.

Integral equation theory for a mixture of spherical and patchy colloids: analytical description.

Publisher Summary Modern statistical-mechanical theories of liquids and dense fluids are based on the calculation of distribution functions, which describe the average structure of the system. The major theoretical question to be answered is given the intermolecular potential between the molecules in the system, what will the structure of the system be at a given thermodynamic state point. Usually it is assumed that the intermolecular potential is pair-wise additive, with the consequence that only the pair structure is needed to describe all the thermodynamic properties of interest. Although the assumption of pair-wise additivity is not valid at high densities and low temperatures, it proves to be a good approximation in most instances. Intermolecular pair potentials are frequently parameterized to take into account higher-order interactions. This chapter focuses on the integral-equation approach to determining the structure of a fluid and therefore its thermodynamic properties and equation of state.

6 Equations of state from analytically solvable integral equation approximations

Erratum: Fluidity of Hydration Layers Nanoconfined between Mica Surfaces [Phys. Rev. Lett. 94 , 026101 (2005)]

Nonequilibrium molecular dynamics calculations of the shear viscosity of supercritical carbon dioxide along the 313 K isotherm are reported. Three different intermolecular potential models of increasing complexity are considered: a spherically symmetric Lennard-Jones potential, a two-site Lennard-Jones potential, and a three-site potential which includes a quadrupole-quadrupole moment. Results for the three potentials are compared with experimental data.

Nonequilibrium molecular dynamics calculation of the shear viscosity of carbon dioxide

Cross-linked chemisorbed n-alkylsilane (CH3(CH2)n-1Si(OH)3) monolayers on amorphous silica surfaces have been studied and their structural properties and frictional performance were compared to those of equivalent monolayers without cross-linkages. The simulations isolated for the first time the effects of both siloxane cross-linkages and the fraction of chains chemisorbed to the surface, providing insight into a longstanding fundamental question in the literature regarding molecular-level structure. The results demonstrate that both cross-linkages and the fraction of chemisorbed chains affect monolayer structure in small but measurable ways, particularly for monolayers constructed from short chains; however, these changes do not appear to have a significant impact on frictional performance.

Peter T. Cummings

Papers

Integral equation theory for a mixture of spherical and patchy colloids: analytical description.

6 Equations of state from analytically solvable integral equation approximations

Erratum: Fluidity of Hydration Layers Nanoconfined between Mica Surfaces [Phys. Rev. Lett. 94 , 026101 (2005)]

Nonequilibrium molecular dynamics calculation of the shear viscosity of carbon dioxide

Investigation of the Impact of Cross-Polymerization on the Structural and Frictional Properties of Alkylsilane Monolayers Using Molecular Simulation