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

An N⋅log(N) method for evaluating electrostatic energies and forces of large periodic systems is presented. The method is based on interpolation of the reciprocal space Ewald sums and evaluation of the resulting convolutions using fast Fourier transforms. Timings and accuracies are presented for three large crystalline ionic systems.

Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems

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

CHARMM (Chemistry at HARvard Macromolecular Mechanics) is a highly flexible computer program which uses empirical energy functions to model macromolecular systems. The program can read or model build structures, energy minimize them by first- or second-derivative techniques, perform a normal mode or molecular dynamics simulation, and analyze the structural, equilibrium, and dynamic properties determined in these calculations. The operations that CHARMM can perform are described, and some implementation details are given. A set of parameters for the empirical energy function and a sample run are included.

CHARMM: A program for macromolecular energy, minimization, and dynamics calculations

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.

/pdf/scalable-molecular-dynamics-with-namd-51o1z7rwp8.pdf

Scalable molecular dynamics with NAMD

Recently, the everimproving cryo-electron microscopy maps of the 70S ribosome have increased the overall accuracy of the modeling studies. This chapter talks about three important structure-function relationships. First, it briefly reviews the recently published model of interactions between the 16S rRNA decoding site and the mRNAtRNA complex. Second, it discusses the functional implications of the placement of that model in the electron density map. Finally, it identifies regions that the authors believe compose the ‘‘gate’’ that closes to form the channel in which the mRNA is located. The second-generation models incorporate atomic-resolution data for those components whose structures have been determined by crystallography or nuclear magnetic resonance (NMR), and for selected components the authors have modeled at atomic detail because of their functional significance. The authors therefore predict that the density in the channel will rise when tRNA is bound at the A site. Another interesting aspect of this model is that the axis of the decoding-site RNA lies perpendicular to the long axis of the 30S ribosomal subunit. Cross-linking studies between mRNA and the 16S rRNA also suggest that these two regions of the 16S rRNA are close together in the ribosomal subunit. Multiscale modeling permits investigation of structure-function relationships at atomic detail within the low-resolution framework of those regions that are less well defined and less functionally significant.

Functional Interpretation of the Cryo-Electron Microscopy Map of the 30S Ribosomal Subunit from Escherichia coli

Correlated motions in proteins arising from the collective movements of residues have long been proposed to be fundamentally important to key properties of proteins, from catalysis and allostery to evolvability. Recent breakthroughs in structural biology have made it possible to capture proteins undergoing complex conformational changes, yet the subtle and intrinsic fluctuations within a single conformation remain one of the least understood facets of protein structure. For many decades, the analysis of diffuse X‐ray scattering held the promise of animating crystal structures with such correlated motions. With recent advances in both X‐ray detectors, this long‐held promise can now be met. In this talk, I’ll describe our recent work in interpreting this signal and discuss how it can be used to the understand the role of correlated motions in enzymes.

Correlated motions in enzymes

Calculs Xα-VB-SW sur Fe(SR) 4 avec R=H ou CH 3 , Fe 2 S 2 (SH) 4 n− (n=2 ou 3), Fe 4 S 4 (SCH 3 ) 4 n− (avec n=2 ou 3)

Models for ferredoxins: electronic structures of iron-sulfur clusters with one, two, and four iron atoms

Kinetik stereochemischer umlagerungen von gemischten beta-diketonato-komplexen des aluminiums(iii)

Calculs par la methode Xα-SW relativiste sur ce complexe a liaison metal-metal quadruple: les effets relativistes sont peu importants

David A. Case

Papers

Functional Interpretation of the Cryo-Electron Microscopy Map of the 30S Ribosomal Subunit from Escherichia coli

Correlated motions in enzymes

Models for ferredoxins: electronic structures of iron-sulfur clusters with one, two, and four iron atoms

Kinetik stereochemischer umlagerungen von gemischten beta-diketonato-komplexen des aluminiums(iii)

Electronic structure of octachloroditungstate(ii)