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.

Temperature and Density Effects on an SN2 Reaction in Supercritical Water

Sites at which excess electrons in pure water at 10 °C could become initially localized and subsequently rapidly solvated are identified by scanning a molecular dynamics simulation of pure equilibrium ST2 water with a test charge. Very favorable sites with respect to both volume and electrostatic potential are found in relatively high number density. Although the observed distribution of large cavities spans a wide range with respect to the electrostatic potential at the cavity centers, the calculated potential energy at the most favorable sites is almost as large as the apparent hydration energy of the electron in the equilibrated state.

Electron localization in liquid water: A computer simulation study of microscopic trapping sites

We present a detailed geometrical analysis of the solvent in an aqueous solution containing two nonpolar atomic solutes which are constrained to an interatomic distance corresponding to a solvent‐separated free energy minimum. The results are obtained from a molecular dynamics simulation using ST2 water. The interpretation of structural features attributed to the hydrophobic effect are facilitated by a time averaging procedure which removes the high frequency librational excitation from the underlying liquid structure. Solvent reordering within the hydration shell surrounding the solutes is clearly revealed by octahedral resolution of orientational correlations and is consistent with the widespread view of ‘‘clathrate‐like’’ structure promotion induced by apolar moieties. Of particular interest, the relatively lengthy simulation reveals a rich variety of cage‐like solvation shell structures which encompass the solvent separated solute particles. The librational freedom of the shell molecules is briefly ex...

The equilibrium solvation structure for the solvent‐separated hydrophobic bond

A direct integration of quantum decoherence into the mixed quantum-classical (MQC) molecular dynamics (MD) method mean field with surface hopping (MF/SH) is explored from the context of the aqueous solvated electron system. Within this framework, the time evolution of the reduced density matrix via the MQC Liouville–von Neumann equation includes dissipation of the off-diagonal elements according to some prescribed decoherence time scale. This fixed parameter corresponds, for example, to the characteristic thermal average decay time of nuclear overlaps of the bath. The MF/SH implementation includes decoherence only within the evolution of the primary subsystem that is responsible for transition probabilities but not within the auxiliary equations governing environmental molecular dynamics. Within this implementation, adiabatic MQC propagation is independent of decoherence rate, and only transition times are affected. Simulations with an average decoherence parameter of 6 fs extend the excited-state lifetim...

Peter J. Rossky

Papers

Temperature and Density Effects on an SN2 Reaction in Supercritical Water

Electron localization in liquid water: A computer simulation study of microscopic trapping sites

The equilibrium solvation structure for the solvent‐separated hydrophobic bond

Dissipative mixed quantum-classical simulation of the aqueous solvated electron system

Quantum mechanical contributions to the structure of liquid water