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

Gibbs ensemble simulation of mixed solvent electrolyte solutions

Thermal and connectivity properties of the Yukawa square-well m-point (YSWmP) model of the network forming fluid are studied using solution of the multidensity Ornstein-Zernike and connectedness Ornstein-Zernike equations supplemented by the associative mean spherical approximation (AMSA). The model is represented by the multicomponent mixture of Yukawa hard spheres with $m_{s}^{a}$
 square-well sites, located on the surface of each hard sphere. To validate the accuracy of the theory, computer simulation is used to calculate the structure, thermodynamic and connectivity properties of the one-component YSW4P version of the model which is compared against corresponding theoretical data. In addition, connectivity properties of the model were studied using Flory-Stockmayer (FS) theory. Predictions of the AMSA for the thermal properties of the model (radial distribution functions (RDF), internal energy, pressure, fractions of the particles in different bonding states) are in good agreement with computer simulation predictions. Similarly, good agreement was found for the connectedness RDF (CRDF), except for the statepoints located close to the percolation threshold, where the theory fails to reproduce the long-range behavior of the CRDF. Results of both theories (AMSA and FS) for the mean cluster size are reasonably accurate only at low degrees of association. Predictions of the FS theory for the percolation lines are in a good agreement with computer simulation predictions. AMSA predictions of percolation are much less accurate, where corresponding percolation lines are located at a temperatures approximately 25% lower then those calculated using computer simulation.

Network Forming Fluids: Yukawa Square-Well m -Point Model

The adiabatic nuclear and electronic sampling method (ANES), originally formulated as an efficient Monte Carlo algorithm for systems with fluctuating charges, is applied to the simulation of a polarizable water model with induced dipole moments. Structural, thermodynamic and dipolar properties obtained by ANES and a newer algorithm, the pair approximation for polarization interaction (PAPI), are compared with full iteration. With the best parameters, the inaccuracy of both approximate methods was found to be comparable with the uncertainty of the full iteration. The PAPI method with iteration radius equal to the second minimum of the oxygen—oxygen correlation function is, depending on the convergence tolerance, 10–15 times faster than the full iteration for 256 molecules, and yields very accurate structure and thermodynamics with deviation about 0.3%. When the iteration radius is increased to the cutoff distance, exact results are recovered at the cost of decreased efficiency. The ANES method with small n...

https://www.prf.jcu.cz/data/files/87/218papi2.pdf

Pair approximation for polarization interaction and adiabatic nuclear and electronic sampling method for fluids with dipole polarizability

A fundamental understanding of interfacial processes in nano-confined ionic liquids is crucial to increase the performance of modern energy storage devices. It is well-known that interfaces between electrodes and ionic liquids exhibit structures distinct from that of the bulk liquid. Following the recent interest in these systems, we studied the structure of thin ionic liquid films confined in flexible uncharged carbon nano-pores by using fully-atomistic molecular dynamics simulations. We show that the interfacial ions self-assemble into a closely-packed chequerboard-like pattern, formed by both cations and anions in direct contact with the pore wall, and that within this structure we find changes dependent on the thickness of the confined films. At low coverages a dense layer is formed in which both the imidazolium-ring and its alkyl-tail lie parallel to the pore wall. With increasing coverage the alkyl-chains reorient perpendicular to the surface, making space for additional ions until a densified highly ordered layer is formed. This wall-induced self-patterning into interfacial layers with significantly higher than bulk density is consistent with recent experimental and theoretical studies of similar systems. This work reveals additional molecular-level details on the effect of the film-thickness on the structure and density of the ionic liquid.

Thickness-dependent structural arrangement in nano-confined imidazolium-based ionic liquid films

Simulation de l'ejection rapide a partir d'un solide amorphe faiblement lie aux densites d'excitation elevees, a l'aide de la dynamique moleculaire afin de comprendre l'ejection d'un volume du materiau par des ions lourds rapides. Calcul de l'ejection des molecules diatomiques d'un solide comme reponse a une grande quantite d'energie deposee dans l'excitation vibrationnelle de ces molecules a l'interieur d'un petit cylindre: la «trace» des ions incidents. Les calculs sont effectues pour deux modes de l'excitation vibrationnelle et pour des echantillons ayant des geometries, des densites numeriques, des energies de cohesion, des epaisseurs, et des conditions aux limites differentes

Peter T. Cummings

Papers

Gibbs ensemble simulation of mixed solvent electrolyte solutions

Network Forming Fluids: Yukawa Square-Well m -Point Model

Pair approximation for polarization interaction and adiabatic nuclear and electronic sampling method for fluids with dipole polarizability

Thickness-dependent structural arrangement in nano-confined imidazolium-based ionic liquid films

Molecular-dynamics simulation of prompt sputtering of a molecular solid at high excitation densities.