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 transient absorption spectroscopy of photoexcited equilibrium hydrated electrons is computed from quantum nonadiabatic molecular dynamics simulations. The results strongly parallel ultrafast spectral transients measured in recent experiments (Barbara and co-workers, J. Chem. Phys. 1993, 98, 5996 and J. Phys. Chem., in press), with spectral dyanmics that cannot be adequately described by a simple two-state kinetic model. Computed transient spectra with various absorption and bleaching contributions removed are used to explore the microscopic physics underlying the complex behavior

Dynamic Elements of Transient Spectral Hole Burning of the Hydrated Electron

Molecular dynamics simulation has been used to explore the nature of solvation dynamics for an excess electron in methanol and in water. We perform the analysis within the linear response theory and show that nonlinear corrections are small in both cases. The response function characterizing solvent relaxation after electron photoexcitation and that following the subsequent nonradiative transition are modeled and found to behave very similarly in methanol, in contrast to water. For methanol, each is comprised of an extremely short Gaussian inertial component of small amplitude and a bi-exponential diffusive decay. A relatively fast ∼1 ps exponential accounts for approximately half of the solvent relaxation and is followed by a slower ∼7 ps relaxation of comparable magnitude, a solvation response that is rather similar to that reported previously for relatively large molecules in methanol. Spectral densities of energy gap fluctuations for the equilibrium ground and excited state trajectories show that translational motion dominates solvation. Relaxational processes in methanol have been compared with the results for water. In contrast to methanol, librational motions of solvent molecules significantly influence aqueous solvation dynamics, especially following excited state decay. This difference is reflected in the relaxational processes, which are an order of magnitude slower in methanol than in water.

Solvation dynamics of an excess electron in methanol and water

Evaluation of Reaction Free Energy Surfaces in Aqueous Solution: An Integral Equation Approach

To model the structure of a urea molecule in aqueous solution including adaption of the solute electronic structure, we have used the reference interaction site model−self-consistent-field (RISM-SCF) method, describing the solute electronic structure at the ab initio level and hydration via an integral equation for the solvent distribution. The RISM-SCF model for aqueous urea gives a clearly nonplanar urea structure, with more than seven waters located within a contact distance defined for hydrogen bonding. The pyramidalization at the urea nitrogen sites is reduced in water relative to the gas phase, but the structure is closer to the gas phase structure than to the planar crystal structure. It is further shown that the solvent produces substantial polarization of the urea solute, with the dipole moment increasing from 4 to 7 D as the geometry and electronic structure are optimized to the aqueous environment. The overall result is to favor a high density of hydrogen bonds between urea and the surrounding ...

A theoretical investigation of the shape and hydration properties of aqueous urea: Evidence for nonplanar urea geometry

The Feynman-Kleinert Linearized Path Integral (FK-LPI) representation of quantum correlation functions is extended in applications and algorithms. Diffusion including quantum effects for a flexible simple point charge model of liquid water is explored, including new tests of internal consistency. An ab initio quantum correction factor (QCF) is also obtained to correct the far-infrared spectrum of water. After correction, a spectrum based on a classical simulation is in good agreement with the experiment. The FK-LPI QCF is shown to be superior to the so-called harmonic QCF. New computational algorithms are introduced so that the quantum Boltzmann Wigner phase-space density, the central object in the implementation, can be obtained for arbitrary potentials. One scheme requires only that the standard classical force routine be replaced when turning from one molecular problem to another. The new algorithms are applied to the calculation of the Van Hove spectrum of liquid He(4) at 27 K. The spectrum moments are in very good agreement with the experiment. These observations indicate that the FK-LPI approach can be broadly effective for molecular problems involving the dynamics of light nuclei.

Peter J. Rossky

Papers

Dynamic Elements of Transient Spectral Hole Burning of the Hydrated Electron

Solvation dynamics of an excess electron in methanol and water

Evaluation of Reaction Free Energy Surfaces in Aqueous Solution: An Integral Equation Approach

A theoretical investigation of the shape and hydration properties of aqueous urea: Evidence for nonplanar urea geometry

Feynman-Kleinert Linearized Path Integral (FK-LPI) Algorithms for Quantum Molecular Dynamics, with Application to Water and He(4).