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

Modularly invariant equations of motion are derived that generate the isothermal–isobaric ensemble as their phase space averages. Isotropic volume fluctuations and fully flexible simulation cells as well as a hybrid scheme that naturally combines the two motions are considered. The resulting methods are tested on two problems, a particle in a one‐dimensional periodic potential and a spherical model of C60 in the solid/fluid phase.

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Constant pressure molecular dynamics algorithms

Nose has derived a set of dynamical equations that can be shown to give canonically distributed positions and momenta provided the phase space average can be taken into the trajectory average, i.e., the system is ergodic [S. Nose, J. Chem. Phys. 81, 511 (1984), W. G. Hoover, Phys. Rev. A 31, 1695 (1985)]. Unfortunately, the Nose–Hoover dynamics is not ergodic for small or stiff systems. Here a modification of the dynamics is proposed which includes not a single thermostat variable but a chain of variables, Nose–Hoover chains. The ‘‘new’’ dynamics gives the canonical distribution where the simple formalism fails. In addition, the new method is easier to use than an extension [D. Kusnezov, A. Bulgac, and W. Bauer, Ann. Phys. 204, 155 (1990)] which also gives the canonical distribution for stiff cases.

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Nosé-Hoover chains : the canonical ensemble via continuous dynamics

The Trotter factorization of the Liouville propagator is used to generate new reversible molecular dynamics integrators This strategy is applied to derive reversible reference system propagator algorithms (RESPA) that greatly accelerate simulations of systems with a separation of time scales or with long range forces The new algorithms have all of the advantages of previous RESPA integrators but are reversible, and more stable than those methods These methods are applied to a set of paradigmatic systems and are shown to be superior to earlier methods It is shown how the new RESPA methods are related to predictor–corrector integrators Finally, we show how these methods can be used to accelerate the integration of the equations of motion of systems with Nose thermostats

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Reversible multiple time scale molecular dynamics

Explicit reversible integrators, suitable for use in large-scale computer simulations, are derived for extended systems generating the canonical and isothermal-isobaric ensembles. The new methods are compared with the standard implicit (iterative) integrators on some illustrative example problems. In addition, modification of the proposed algorithms for multiple time step integration is outlined.

Explicit reversible integrators for extended systems dynamics

A new reciprocal space based formalism for treating long range forces in clusters is presented. It will be shown how the new formalism can be incorporated into plane-wave based density function theory calculations, standard Ewald summation calculations, and smooth particle-mesh Ewald calculations to yield accurate and numerically efficient descriptions of long range interactions in cluster systems.

Glenn J. Martyna

Papers

Constant pressure molecular dynamics algorithms

Nosé-Hoover chains : the canonical ensemble via continuous dynamics

Reversible multiple time scale molecular dynamics

Explicit reversible integrators for extended systems dynamics

A reciprocal space based method for treating long range interactions in ab initio and force-field-based calculations in clusters