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 develop extensions to a previous methodology for evaluating the excess compressibility of solvation. These extensions make it possible to analyze solution compressibilities in terms of the hydration shell model of solvation. The methodology is applied to three model soluteswater, methane, and methanolin water. We find that the compressibility is accounted for by localized effects of the solute on the solvent. In addition, for the case of methanol, we find that the localized effects of one solute functional group are independent of the effects of the other. This creates the opportunity for estimation of group-additive contributions to the compressibility, and we illustrate a technique for the extraction of such contributions from molecular dynamics simulation data. The technique is easily generalized for examination of large solutes, including biologically important macromolecules.

Evaluation of Functional Group Contributions to Excess Volumetric Properties of Solvated Molecules

Non-linear response and hydrogen bond dynamics for electron solvation in methanol

The microscopic connections between solvation dynamics and the experimentally measured dynamic emission Stokes shift are explored by molecular dynamics simulation using the hydrated electron as a fully quantum mechanical probe. Solvent response functions are computed using the method of spectral reconstruction at various time resolutions for both fluorescence and stimulated emission and compared directly to the dynamic evolution of the underlying electronic energy gap. The first spectral moment proves to be a better choice of characteristic frequency than the spectral maximum, and iterative deconvolution is found to significantly improve the spectrally determined solvent response function. Use of the appropriate characteristic frequency at zero time to produce solvent response functions which do not start at unity further improves the agreement between the spectrally determined and microscopic solvent response functions.

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An Exploration of the Relationship between Solvation Dynamics and Spectrally Determined Solvent Response Functions by Computer Simulation

Influence of an antiviral compound on the temperature dependence of viral protein flexibility and packing: a molecular dynamics study.

The optoelectronic properties of amorphous conjugated polymers are sensitive to the details of the conformational disorder, and spectroscopy provides the means for structural characterization of the fragments of the chain that interact with light—“chromophores”. A faithful interpretation of spectroscopic conformational signatures, however, presents a theoretical challenge. Here we investigate the relationship between the ground-state optical gaps, the properties of the excited states, and the structural features of chromophores of a single molecule poly(3-hexyl)-thiophene (P3HT) using quantum–classical atomistic simulations. Our results demonstrate that chromophoric disorder arises through the interplay between excited-state delocalization and electron–hole polarization, controlled by the torsional disorder introduced by side chains. Within this conceptual framework, we predict and explain the counterintuitive spectral behavior of P3HT, a red-shifted absorption, despite shortening of chromophores, with in...

Peter J. Rossky

Papers

Evaluation of Functional Group Contributions to Excess Volumetric Properties of Solvated Molecules

Non-linear response and hydrogen bond dynamics for electron solvation in methanol

An Exploration of the Relationship between Solvation Dynamics and Spectrally Determined Solvent Response Functions by Computer Simulation

Influence of an antiviral compound on the temperature dependence of viral protein flexibility and packing: a molecular dynamics study.

Relating Chromophoric and Structural Disorder in Conjugated Polymers.