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

With the use of the grand canonical Monte Carlo simulation, water adsorption isotherms were determined for SPC/E water in slit-shaped graphitic nanopores at 298 K The pore widths considered were 06, 0625, 07, 08, 10, 16, and 20 nm The resulting adsorption isotherms indicated negligible adsorption at low pressures, pore-filling by a capillary-condensation-like mechanism, and adsorption/desorption hysteresis loops For pore widths equal to or larger than 07 nm, the relative pressure at which pore filling occurs and the size of the hysteresis loop decrease with decreasing pore width For 06-nm pores, pore filling occurs at pressures approaching saturation Upon decreasing the pore width from 20 to 07 nm, the zero-coverage isosteric heat of adsorption increases from 6 to 14 kJ/mol The limit at high coverage converges to the enthalpy of condensation for SPC/E water as the pore width increases From the simulated adsorbed-water densities and distributions across the pores and the use of a mean-fie

Water Adsorption in Carbon-Slit Nanopores

Classical molecular dynamics (CMD) simulations of the (1011) surface of quartz interacting with bulk liquid water are performed using three different classical force fields, Lopes et al., ClayFF, ...

Simulations of the Quartz(1011)/Water Interface: A Comparison of Classical Force Fields, Ab Initio Molecular Dynamics, and X-ray Reflectivity Experiments

We perform molecular dynamics simulations to investigate the shear dynamics of hydration water nanoconfined between two mica surfaces at 1 bar pressure and 298 K. Newtonian plateaus of shear viscosity comparable to the bulk value for different hydration layers D=0.92-2.44 nm are obtained. The origin of this persistent fluidity of the confined aqueous system is found to be closely associated with the rotational dynamics of water molecules, accompanied by fast translational diffusion under this confinement.

Fluidity of hydration layers nanoconfined between mica surfaces.

The precision of several methods for computing the chemical potential by molecular simulation is investigated. The study does not apply molecular simulation to the analysis but instead works with models of the simulation process. These models enable the variance of the chemical potential to be computed accurately and very quickly and thereby permits the methods (freeenergy perturbation, expanded ensembles, thermodynamic integration, and histogram-distribution methods) to be optimized and compared over a range of densities. The study focuses exclusively on the hard-sphere model. This model is simple and well characterized; yet it exhibits the essential features that make the chemical potential calculation difficult; arguments are presented to support the broader applicability of the study. The severe asymmetry of particle insertion against particle deletion is highlighted, and it is shown that any staged free-energy perturbation method with a 'deletion' component is highly prone to systematic error. More g...

Quantitative comparison and optimization of methods for evaluating the chemical potential by molecular simulation

Computer simulations of double-walled carbon nanotubes show that if the inner nanotube is pulled out part of the way and then released, then the inner tube exhibits damped oscillatory behavior at gigahertz frequencies. A simple mathematical model, formulated in terms of macroscopic ideas of friction, is shown to predict the observed behavior to a high degree of accuracy.

Peter T. Cummings

Papers

Water Adsorption in Carbon-Slit Nanopores

Simulations of the Quartz(1011)/Water Interface: A Comparison of Classical Force Fields, Ab Initio Molecular Dynamics, and X-ray Reflectivity Experiments

Fluidity of hydration layers nanoconfined between mica surfaces.

Quantitative comparison and optimization of methods for evaluating the chemical potential by molecular simulation

Oscillatory Behavior of Double-Walled Nanotubes under Extension: A Simple Nanoscale Damped Spring