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

Using nonequilibrium molecular dynamics simulation, we have studied the response of a C100 model polymer melt to a step change from equilibrium to a constant, high shear rate flow. The transient shear stress of the model polymer melt exhibits pronounced overshoot at the strain value predicted by the reptation model, in striking similarity to melts of longer, entangled polymer governed by reptation motion. At the maximum of shear stress overshoot, the molecular orientational order and the alignment angle are found to be midway between those characteristic of Newtonian flow and full alignment with the flow. The Doi-Edwards theory is found to be applicable but only by taking into account the shear-rate-dependence of the terminal relaxation time. We further analyze the molecular origins of such behavior in short polymer chains by decomposing the total stress into the contributions from various molecular interactions. @S1063-651X~99!08911-4# PACS number~s!: 83.20.Jp, 83.20.Di, 83.20.Fk, 83.50.By The rheological properties of a liquid of short, unentangled polymer chains at high shear rate are still not well understood. Experimental data are unavailable because of the difficulty of reaching the nonlinear viscoelastic regime in shear rate for short-chain systems. On the theoretical side, a successful theory of the rheological properties of short-chain polymers in the nonlinear regime has not been developed. The Rouse model is generally considered to provide a good description of the linear-response dynamics of short-chain polymeric systems in the liquid state @1#. This is substantiated by a large body of experimental work and molecular simulation results. Recent computer simulation studies sug

Transient rheology of a polyethylene melt under shear.

We present nonequilibrium molecular dynamics simulations of pure argon at a temperature of 135 K and density of 1.034 gm/cc using the highly accurate Barker–Fisher–Watts (BFW) model for the intermolecular potential. We consider the BFW potential both with and without the Axilrod–Teller three‐body interaction. We find that the three‐body potential has a very small effect on the shear viscosity: The predicted value in the presence of three‐body forces is 3% less than that obtained without three‐body forces.

Effect of three‐body forces on the shear viscosity of liquid argon

The stress-stress correlation function and the viscosity of a united-atom model of liquid decane are studied by equilibrium molecular dynamics simulation using two different formalisms for the stress tensor: the atomic and the molecular formalisms. The atomic and molecular correlation functions show dramatic difference in short-time behaviour. The integrals of the two correlation functions, however, become identical after a short transient period which is significantly shorter than the rotational relaxation time of the molecule. Both reach the same plateau value in a time period corresponding to this relaxation time. These results provide a convenient guide for the choice of the upper integral time limit in calculating the viscosity by the Green-Kubo formula.

The calculation of the viscosity from the autocorrelation function using molecular and atomic stress tensors

The tribology of 2-methacryloyloxyethyl phosphorylcholine monolayers in water is studied using molecular dynamics simulations. Our results show two distinct shear regimes where the first is dominated by hydration lubrication, exhibiting near zero friction coefficients, and the second by chain-chain interactions, resembling monomer-supported lubrication. These results provide insight into the hydration lubrication mechanism - a phenomena thought to underlie the extremely efficient lubrication provided by surfaces functionalized with polyzwitterionic polymer brushes and the mammalian synovial joint.

/pdf/tunable-transition-from-hydration-to-monomer-supported-2np0v7fc16.pdf

Tunable transition from hydration to monomer-supported lubrication in zwitterionic monolayers revealed by molecular dynamics simulation

The mechanism of the formation of different junction structures of gold nanowires under stretching has been studied by comprehensive molecular dynamics (MD) simulations using the second-moment approximation of the tight-binding (TB-SMA) potential. The simulations (540 MD runs in total) reveal that there is an inherent rate-dependent energy release law that unifies the effects of the system size, the temperature, and elongation rate on the dynamic elongations of gold nanowires.

Peter T. Cummings

Papers

Transient rheology of a polyethylene melt under shear.

Effect of three‐body forces on the shear viscosity of liquid argon

The calculation of the viscosity from the autocorrelation function using molecular and atomic stress tensors

Tunable transition from hydration to monomer-supported lubrication in zwitterionic monolayers revealed by molecular dynamics simulation

Rate-dependent energy release mechanism of gold nanowires under elongation.