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

: This report reviews the development and applications of molecular and materials modeling in Europe and Japan in comparison to those in the United States. Topics covered include computational quantum chemistry, molecular simulations by molecular dynamics and Monte Carlo methods, mesoscale modeling of material domains, molecular-structure/macroscale property correlations like QSARs and QSPRs, and related information technologies like informatics and special-purpose molecular-modeling computers. The panel's findings include the following: The United States leads this field in many scientific areas. However, Canada has particular strengths in DFT methods and homogeneous catalysis; Europe in heterogeneous catalysis, mesoscale, and materials modeling; and Japan in materials modeling and special-purpose computing. Major government-industry initiatives are underway in Europe and Japan, notably in multi-scale materials modeling and in development of chemistry-capable ab-initio molecular dynamics codes. In European and U.S. assessments of nanotechnology, it was also concluded that to advance the field most quickly and competitively the need is acute for applying new and existing methods of molecularly based modeling. Additional findings are outlined in the panel's executive summary.

Applications of Molecular and Materials Modeling

Vapor-liquid equilibrium and density measurements have been performed on 1.00-5.89 m tetrabutylammonium bromide (TBAB) in mixtures of 2-propanoland water. The VLE experiments were performed using a modified Othmer still at ambient pressure. The effect of salt on the relative volatility of 2-propanol was evaluated at molalities of 1.00,1.79, and 5.89 over the full range of solvent composition. At each salt molality, as the alcohol concentration increased, salting-in and then salting-out behavior of the alcohol was observed. The azeotrope was shifted but apparently not eliminated for the salt concentrations studied. Density measurements at 25,40, and 55 "C were taken using a vibrating tube densimeter at four salt molalities over the full range of solvent composition. As salt molality increases, the apparent molar volume of TBAB exhibits a minimum between 1 to 2 m TBAB in pure water, it is slightly larger and monotonically increases in pure 2-propanol, and it is larger yet, with a maximum at lower 2-propanol amounts, in the ternary mixture.

Vapor-Liquid Equilibria and Salt Apparent Molar Volumes of the Water + 2-Propanol + Tetrabutylammonium Bromide System

The product±reactant Ornstein±Zernike approach, represented by the polymer mean-spherical approximation (PMSA), is utilized to describe the structure and thermodynamic properties of theuid of Yukawa hard sphere chain molecules. An analytical solution of the PMSA for the most general case of the multicomponent freely jointed hard sphere multi-Yukawa chainuid is presented. As in the case of the regular MSA for the hard sphere Yukawauid, the problem is reduced to the solution of a set of nonlinear algebraic equations in the general case, and to a single equation in the case of the factorizable Yukawa potential coeA cients. Closed form analytical expressions are presented for the contact values of the monomer±monomer radial distribution function, structure factors, internal energy, Helmholtz free energy, chemical potentials and pressure in terms of the quantities, which follows directly from the PMSA solution. By way of illustration, several diA erent versions of the hard sphere Yukawa chain model are considered, represented by one-Yukawa chains of length m, where m ˆ 2;4;8;16. To validate the accuracy of the present theory, Monte Carlo simulations were carried out and the results are compared systematically with the theoretical results for the structure and thermodynamic properties of the system at hand. In general it is found that the theory per- forms very well, thus providing an analytical route to the equilibrium properties of a well de®ned model for chainuids.

Structural and thermodynamic properties of a multicomponent freely jointed hard sphere multi-Yukawa chain fluid

A model for simple fluids is proposed in which the radial distribution function has a parametric form appropriate to a soft-core fluid for interparticle separationr ⩽ R, whereR is some range parameter. Forr > R, the direct correlation function is assumed to be of Yukawa form. The Ornstein-Zernike equation is solved for this system, yielding the radial distribution and the total correlation function for the entire range of interparticle separation. Methods of relating the model fluid to a real fluid by assigning values to the parameters are discussed.

Solution of the Ornstein-Zernike equation for a soft-core Yukawa fluid

A straightforward derivation for the configurational temperature associated with the orientational ΩN portion of the configurational phase space of the molecules in an open system is presented. Explicit relationships are given for determining the configurational temperatures in classical simulations of molecular liquids, such as water, and their forms and their evaluation discussed.

Peter T. Cummings

Papers

Applications of Molecular and Materials Modeling

Vapor-Liquid Equilibria and Salt Apparent Molar Volumes of the Water + 2-Propanol + Tetrabutylammonium Bromide System

Structural and thermodynamic properties of a multicomponent freely jointed hard sphere multi-Yukawa chain fluid

Solution of the Ornstein-Zernike equation for a soft-core Yukawa fluid

On the determination of orientational configurational temperature from computer simulation