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

QUANTUM ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling, based on density-functional theory, plane waves, and pseudopotentials (norm-conserving, ultrasoft, and projector-augmented wave). The acronym ESPRESSO stands for opEn Source Package for Research in Electronic Structure, Simulation, and Optimization. It is freely available to researchers around the world under the terms of the GNU General Public License. QUANTUM ESPRESSO builds upon newly-restructured electronic-structure codes that have been developed and tested by some of the original authors of novel electronic-structure algorithms and applied in the last twenty years by some of the leading materials modeling groups worldwide. Innovation and efficiency are still its main focus, with special attention paid to massively parallel architectures, and a great effort being devoted to user friendliness. QUANTUM ESPRESSO is evolving towards a distribution of independent and interoperable codes in the spirit of an open-source project, where researchers active in the field of electronic-structure calculations are encouraged to participate in the project by contributing their own codes or by implementing their own ideas into existing codes.

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QUANTUM ESPRESSO: a modular and open-source software project for quantum simulations of materials

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

NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD scales to hundreds of processors on high-end parallel platforms, as well as tens of processors on low-cost commodity clusters, and also runs on individual desktop and laptop computers. NAMD works with AMBER and CHARMM potential functions, parameters, and file formats. This article, directed to novices as well as experts, first introduces concepts and methods used in the NAMD program, describing the classical molecular dynamics force field, equations of motion, and integration methods along with the efficient electrostatics evaluation algorithms employed and temperature and pressure controls used. Features for steering the simulation across barriers and for calculating both alchemical and conformational free energy differences are presented. The motivations for and a roadmap to the internal design of NAMD, implemented in C++ and based on Charm++ parallel objects, are outlined. The factors affecting the serial and parallel performance of a simulation are discussed. Finally, typical NAMD use is illustrated with representative applications to a small, a medium, and a large biomolecular system, highlighting particular features of NAMD, for example, the Tcl scripting language. The article also provides a list of the key features of NAMD and discusses the benefits of combining NAMD with the molecular graphics/sequence analysis software VMD and the grid computing/collaboratory software BioCoRE. NAMD is distributed free of charge with source code at www.ks.uiuc.edu.

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Scalable molecular dynamics with NAMD

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Scalable Molecular Dynamics with NAMD

An electronically coarse-grained model for water reveals a persistent vestige of the liquid-gas transition deep into the supercritical region. A crossover in the density dependence of the molecular dipole arises from the onset of nonpercolating hydrogen bonds. The crossover points coincide with the Widom line in the scaling region but extend farther, tracking the heat capacity maxima, offering evidence for liquidlike and gaslike state points in a "one-phase" fluid. The effect is present even in dipole-limit models, suggesting that it is common for all molecular liquids exhibiting dipole enhancement in the liquid phase.

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Molecular-scale remnants of the liquid-gas transition in supercritical polar fluids.

The leap-frog based integration algorithms for Nose–Hoover chain dynamics recently presented by Jang and Voth [J. Chem. Phys. 107, 9514 (1997)] are shown to give rise to nonsecular growth in the conserved quantity at long times. Therefore, their use in molecular dynamics simulations should be approached with caution.

Comment on “Simple reversible molecular dynamics algorithms for Nosé–Hoover chain dynamics” [J. Chem. Phys. 107, 9514 (1997)]

The quantum Drude oscillator (QDO) model, which allows many-body polarization and dispersion to be treated both on an equal footing and beyond the dipole limit, is investigated using two approaches to the linear scaling diffusion Monte Carlo (DMC) technique. The first is a general purpose norm-conserving DMC (NC-DMC) method wherein the number of walkers, $N$, remains strictly constant thereby avoiding the sudden death or explosive growth of walker populations with an error that vanishes as $\mathcal{O}({N}^{\ensuremath{-}1})$ in the absence of weights. As NC-DMC satisfies detailed balance, a phase space can be defined that permits both an exact trajectory weighting and a fast mean-field trajectory weighting technique to be constructed which can eliminate or reduce the population bias, respectively. The second is a many-body diagrammatic expansion for trial wave functions in systems dominated by strong on-site harmonic coupling and a dense matrix of bilinear coupling constants such as the QDO in the dipole limit; an approximate trial function is introduced to treat two-body interactions outside the dipole limit. Using these approaches, high accuracy is achieved in studies of the fcc-solid phase of the highly polarizable atom, xenon, within the QDO model. It is found that 200 walkers suffice to generate converged results for systems as large as 500 atoms. The quality of QDO predictions compared to experiment and the ability to generate these predictions efficiently demonstrate the feasibility of employing the QDO approach to model long-range forces.

Norm-conserving diffusion Monte Carlo method and diagrammatic expansion of interacting drude oscillators: Application to solid xenon

Doping of large-pore crown graphene nanomesh

Accordingly, the present invention provides a method of forming an electrode having reduced corrosion and water decomposition on a surface thereof. A substrate which has a conductive layer disposed thereon is provided and the conductive layer has an oxide layer with an exposed surface. The exposed surface of the oxide layer contacts a solution of an organic surface active compound in an organic solvent to form a protective layer of the organic surface active compound over the oxide layer. The protective layer has a thickness of from about 0.5 nm to about 5 nm and ranges therebetween depending on a chemical structure of the surface active compound.

Glenn J. Martyna

Papers

Molecular-scale remnants of the liquid-gas transition in supercritical polar fluids.

Comment on “Simple reversible molecular dynamics algorithms for Nosé–Hoover chain dynamics” [J. Chem. Phys. 107, 9514 (1997)]

Norm-conserving diffusion Monte Carlo method and diagrammatic expansion of interacting drude oscillators: Application to solid xenon

Doping of large-pore crown graphene nanomesh

Forming an electrode having reduced corrosion and water decomposition on surface using an organic protective layer