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

The previously developed particle mesh Ewald method is reformulated in terms of efficient B‐spline interpolation of the structure factors This reformulation allows a natural extension of the method to potentials of the form 1/rp with p≥1 Furthermore, efficient calculation of the virial tensor follows Use of B‐splines in place of Lagrange interpolation leads to analytic gradients as well as a significant improvement in the accuracy We demonstrate that arbitrary accuracy can be achieved, independent of system size N, at a cost that scales as N log(N) For biomolecular systems with many thousands of atoms this method permits the use of Ewald summation at a computational cost comparable to that of a simple truncation method of 10 A or less

A smooth particle mesh Ewald method

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

6.2.2. Definition of Effective Properties 3064 6.3. Response Properties to Magnetic Fields 3066 6.3.1. Nuclear Shielding 3066 6.3.2. Indirect Spin−Spin Coupling 3067 6.3.3. EPR Parameters 3068 6.4. Properties of Chiral Systems 3069 6.4.1. Electronic Circular Dichroism (ECD) 3069 6.4.2. Optical Rotation (OR) 3069 6.4.3. VCD and VROA 3070 7. Continuum and Discrete Models 3071 7.1. Continuum Methods within MD and MC Simulations 3072

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Quantum mechanical continuum solvation models.

We present approximate pseudopotential quantum-mechanical calculations of the excess electron states of equilibrated neutral water clusters sampled by classical molecular dynamics simulations. The internal energy of the clusters are representative of those present at temperatures of 200 and 300K. Correlated electronic structure calculations are used to validate the pseudopotential for this purpose. We find that the neutral clusters support localized, bound excess electron ground states in about 50% of the configurations for the smallest cluster size studied (n=20), and in almost all configurations for larger clusters (n>66). The state is always exterior to the molecular frame, forming typically a diffuse surface state. Both cluster size and temperature dependence of energetic and structural properties of the clusters and the electron distribution are explored. We show that the stabilization of the electron is strongly correlated with the preexisting instantaneous dipole moment of the neutral clusters, and...

/pdf/excess-electron-localization-sites-in-neutral-water-clusters-4kmxleb62e.pdf

Excess electron localization sites in neutral water clusters

In this lecture, aspects of the hydration of hydrophobic interfaces that are emergent nanoscale properties of the interface chemical structure are discussed. General results inferred from systematic computational studies are emphasized, with a central theme focusing on the separate roles of surface topography and surface chemistry. The roles of surface curvature, polarity, and chemical heterogeneity, as well as the important role of solvent thermodynamic state are considered. The potential importance of understanding evolved natural biological interfaces on the same basis as model synthetic surfaces is pointed out, and progress in this direction is discussed.

Exploring nanoscale hydrophobic hydration

The spectrum of the Van Hove correlation function (CF) is calculated for liquid He(4) at 27 K and a density of 0.25 g/cm 3 by utilizing a recently proposed approximation to quantum CFs derived by combining an effective-frequency Boltzmann-Wigner transform with a linearized path integral expression for CFs. For this anharmonic system and highly nonlinear CF, we obtain excellent agreement with available accurate results. In particular, the first, second, and third moments of the spectrum are in very good agreement with both experiment and earlier theoretical results. Also, the calculated kinetic energy is in excellent agreement with accurate path integral Monte Carlo results.

Determination of the Van Hove Spectrum of Liquid He(4): An Application of the Feynman-Kleinert Linearized Path Integral Methodology †

We investigate the microscopic mechanism of cold and heat denaturation using a 3D lattice model of a hydrated protein in which water is represented explicitly. The water model, which incorporates directional bonding and tetrahedral geometry, captures many aspects of water thermodynamics and properly describes hydrophobic hydration around apolar solutes because the hydrogen bonding rules in the model were gleaned from off-lattice atomistic simulations of water around representative protein structures. By incorporating local chain stiffness in the protein model, a homopolymer can fold into a β-hairpin. It is shown that the homopolymer can be folded by either attractive interactions between the monomers or as a direct consequence of the entropic cost of forming interfacial hydrogen bonds in the solvent. However, cold denaturation is not observed if the collapse transition is induced by intramolecular attractions. We further find that it is the changes in hydrophobic hydration with decreasing temperature that drive cold unfolding and that the overall process is enthalpically driven, whereas heat denaturation is entropically driven.

Peter J. Rossky

Papers

Excess electron localization sites in neutral water clusters

Exploring nanoscale hydrophobic hydration

Determination of the Van Hove Spectrum of Liquid He(4): An Application of the Feynman-Kleinert Linearized Path Integral Methodology †

Role of Hydrophobic Hydration in Protein Stability: A 3D Water-Explicit Protein Model Exhibiting Cold and Heat Denaturation

Hydration structure of the α-chymotrypsin substrate binding pocket: the impact of constrained geometry