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

Details of structural changes that take place in water near an apolar solute have been studied by Monte Carlo simulations for hard sphere solutes of increasing size, including the limiting case of water at a hard structureless wall. Water has been modelled by two diA erent types of extended primitive model, the four-site EPM4 model and ®ve-site EPM5 model. Two diA erent patterns of the orientational ordering of the water molecules around the solute as a function of its size have been found. For the EPM5 model, the structure of water and the orientation of its molecules near an apolar solute of ®nite diameter do not seem to be sensitive to the size of the solute, and only become more pronounced when the solute becomes a hard wall. On the other hand, the orientation ordering of the EPM4 molecules gradually changes with increasing size of the solute, and for solutes larger than approximately ®ve times the size of the water molecule it is opposite to that near a small solute. A novel method to evaluate the excess chemical potential of large solutes has been implemented, and some thermodynamic quantities for water (distribution of hydrogen bonds and the excess chemical potential) have been computed as a function of the distance from the solute.

https://www.prf.jcu.cz/data/files/87/215mp-hh2.pdf

Hydrophobic hydration at the level of primitive models. II: Large solutes and water restructuring

A new method is presented for the Monte Carlo simulations of polarizable models with induced dipole moments. This method updates induced dipole moments on all molecules when a single molecule is moved, without evaluating all pair interactions. Thus, depending on the number of molecules, it is 10–20 times faster than Monte Carlo simulations with full iteration. The efficiency makes it a powerful tool for the study of phase equilibria of polarizable models in grand canonical and Gibbs ensembles.

Pair approximation for polarization interaction: efficient method for Monte Carlo simulations of polarizable fluids

We use nonequilibrium molecular-dynamics (NEMD) simulations to characterize the response of a fluid subjected to an electric field. We focus on the response for very weak fields. Fields accessible by conventional NEMD methods are typically of the order of 109Vm−1, i.e., several orders of magnitude larger than those typically used in experiments. Using the transient time-correlation function, we show how NEMD simulations can be extended to study systems subjected to a realistic dc electric field. We then apply this approach to study the response of molten sodium chloride for a wide range of dc electric fields.

Conductivity of molten sodium chloride in an arbitrarily weak dc electric field

EditorialJoint Statement of Editors of Journals Publishing Thermophysical Property Data: Process for Article Submission for The Journal of Chemical Thermodynamics, Fluid Phase Equilibria, International Journal of Thermophysics, Thermochimica Acta, and Journal of Chemical Engineering Data

The product-reactant Ornstein–Zernike approach, supplemented by the ideal network approximation, is formulated for the Yukawa sticky m-point (YSmP) model of associating fluid. The model is represented by the multicomponent mixture of the Yukawa hard spheres with m sticky points randomly located on the surface of each hard sphere. Extensions of the regular integral equation closures, which include polymer Percus–Yevick, polymer hypernetted chain and polymer mean spherical approximations, are presented. An analytical solution of the polymer mean spherical approximation is derived and closed form analytical expressions for the structure (contact value of the radial distribution function, structure factor) and thermodynamic (internal energy) properties of the YSmP model are obtained. Due to generality and flexibility of the model it can be used to study the properties of a number of different associating fluids, including water and aqueous solutions. By way of illustration liquid–gas phase diagrams for the model with m=0, 1, 2, 3, 4 are presented and discussed. Predictions of the theory for the liquid–gas phase diagram of the YS4P model with the parameters similar to those assumed in the frames of the statistical associating fluid theory to mimic water are in reasonably good agreement with the corresponding experimental data for water.

Peter T. Cummings

Papers

Hydrophobic hydration at the level of primitive models. II: Large solutes and water restructuring

Pair approximation for polarization interaction: efficient method for Monte Carlo simulations of polarizable fluids

Conductivity of molten sodium chloride in an arbitrarily weak dc electric field

EditorialJoint Statement of Editors of Journals Publishing Thermophysical Property Data: Process for Article Submission for The Journal of Chemical Thermodynamics, Fluid Phase Equilibria, International Journal of Thermophysics, Thermochimica Acta, and Journal of Chemical Engineering Data

Yukawa sticky m-point model of associating fluid