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.

The role of quantum coherence loss in mixed quantum-classical dynamical systems is explored in the context of the theory of quantum decoherence introduced recently by Bittner and Rossky [J. Chem. Phys. 103, 8130 (1995)]. This theory, which is based upon the consistent histories interpretation of quantum mechanics, introduces decoherence in the quantum subsystem by carefully considering the relevant time and length scales over which one must consider the effects of phase interference between alternative histories of the classical subsystem. Such alternative histories are an integral part of any quantum-classical computational scheme which employs transitions between discrete quantum states; consequently, the coherences between alternative histories have a profound effect on the transition probability between quantum states. In this paper, we review the Bittner–Rossky theory and detail a computational algorithm suitable for large-scale quantum molecular dynamics simulations which implements this theory. Application of the algorithm towards the relaxation of a photoexcited aqueous electron compare well to previous estimates of the excited state survival time as well as to the experimental measurements.

Decoherent histories and nonadiabatic quantum molecular dynamics simulations

An electronic state and nuclear configuration dependent mechanism for electronic coherence loss is integrated into the mean field with surface hopping (MF/SH) algorithm for nonadiabatic (NA) mixed quantum–classical molecular dynamics (MQC-MD). The characteristic decoherence time scale between a pair of states is evaluated from differences in the instantaneous Hellmann–Feynman forces on the two surfaces at each phase space point along the quantum–classical trajectory. Within this instantaneous decoherence mean field with surface hopping (id-MF/SH) formalism, both the primary evolution that is responsible for transition probabilities and the auxiliary equations governing the nuclear dynamics are described by the same dissipative MQC Liouville–von Neumann equation. Decoherence, therefore, impacts both the transition probabilities and the realization of the quantum–classical trajectory. The method is implemented for the solvated electron in water and methanol and applied to trajectories describing photoexcita...

Solvent-induced electronic decoherence: Configuration dependent dissipative evolution for solvated electron systems

Nonadiabatic molecular dynamics simulations are used to analyze the role of different solvent molecular degrees of freedom in the nonradiative relaxation of the first excited state of the hydrated electron. The relaxation occurs through a spatially diffuse multimode coupling between the adiabatic electronic states, indicating that the process cannot be described by a single-mode promotion model frequently used in the “large molecule” limit of gas phase theories. Solvent librations and vibrations, and the H 2O asymmetric stretch in particular, are found to be the most effective promotors of the electronic transition. Dissipation of the released energy to the solvent proceeds on two time scales: a fast 10-20 fs heating of the first solvation shell, where most of the energy is accepted by the librational degrees of freedom, and a several hundred femtosecond global reconstruction of the solvent as the first shell transfers its excess energy to the rest of the molecules. The implications of our use of a semiclassical approximation as the criterion for good promoting and energy dissipating modes are discussed. The majority of chemical processes involve radiationless energy transfer in one or more of their elementary steps, be it an intermolecular conversion, intramolecular relaxation, or an ordinary heating necessary to activate a reaction. The role of nonradiative processes is particularly pronounced in liquid phase chemistry, where the solvent serves as a thermal bath providing or withdrawing energy from the reacting species. During the past decade new experimental and theoretical techniques have been developed allowing for detailed dynamical studies on ultrafast processes in polar solutions. The hydrated electron, being a relatively simple as well as ubiquitous species in solution photo- and electrochemistry, represents a unique system for such studies. Because the hydrated electron is merely an extra electron in pure water, its evolution is governed solely by nuclear motions of water molecules. The instantaneous configuration of the solvent determines the Born-Oppenheimer (B-O) electronic energy spectrum. Vibrations and librations couple these electronic states, leading to nonadiabatic radiationless transitions. The electronic energy released during the transitions is accepted by specific solvent modes, and as the solvation structure approaches equilibrium, the energy is dissipated into the rest of the solvent. The present work was carried out to elucidate in detail what particular solvent motions and solvent regions have the greatest impact on these aspects of hydrated electron relaxation dynamics. This analysis represents the first such

Solvent Mode Participation in the Nonradiative Relaxation of the Hydrated Electron

Application de l'equation integrale d'une chaine hyperreticulee a un systeme modele simple representant un polyion isole fibreux dans une solution electrolytique

Ionic atmosphere of rodlike polyelectrolytes. A hypernetted chain study

Quantum nonadiabatic molecular dynamics simulations are used to explore the molecular details surrounding photoexcitation of solvated electrons in deuterated water. The results are compared to previous studies in normal water [B. J. Schwartz and P. J. Rossky, J. Chem. Phys. 101, 6902, 6917 (1994)] to elucidate the nature of the isotope effect on both the solvation and nonadiabatic relaxation dynamics. The solvent spectral density couples differently to the individual energy levels than to the quantum energy gap, indicating the importance of the symmetry of both the ground and excited states in determining the resulting solvent response. The solvation dynamics are characterized by a Gaussian plus biexponential decay. Deuteration has little effect on the Gaussian component or long time exponential decay of the solvent response function, but a ∼20% isotope effect is observed on the faster exponential decay. The solvent response following nonadiabatic relaxation is found to be much more rapid than that follow...

Peter J. Rossky

Papers

Decoherent histories and nonadiabatic quantum molecular dynamics simulations

Solvent-induced electronic decoherence: Configuration dependent dissipative evolution for solvated electron systems

Solvent Mode Participation in the Nonradiative Relaxation of the Hydrated Electron

Ionic atmosphere of rodlike polyelectrolytes. A hypernetted chain study

The isotope effect in solvation dynamics and nonadiabatic relaxation : a quantum simulation study of the photoexcited solvated electron in d2o