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 consider an approach for describing vibrational energy relaxation processes in liquids for solutes excited to states which are dominated by single-mode excitations. The method utilizes the fact that adding a suitable linear term to the solute intramolecular potential, creates excitations in the first excited state of a chosen vibrational mode. The fully quantum energy decay rate of the vibrational excitation can then be derived using quadratic response theory, which expresses the decay rate as the decay of a second-order Kubo transformed correlation function. This correlation function can be exactly related to a path integral centroid second-order correlation function, which can be evaluated approximately by centroid molecular dynamics. The abilities and limitations of the approach are discussed. It is shown that the method should work best when only a single vibrational state is occupied prior to excitation. Practical matters require also that the relaxation is in the pico-second regime or shorter. In...

A second-order Kubo response theory-centroid approach to vibrational energy relaxation for single-mode excitations

Methanol is an amphiphilic solute whose aqueous solutions exhibit distinctive physical properties. The volume change upon mixing, for example, is negative across the entire composition range, indicating strong association. We explore the corresponding behavior of a Jagla solvent, which has been previously shown to exhibit many of the anomalous properties of water. We consider two models of an amphiphilic solute: (i) a "dimer" model, which consists of one hydrophobic hard sphere linked to a Jagla particle with a permanent bond, and (ii) a "monomer" model, which is a limiting case of the dimer, formed by concentrically overlapping a hard sphere and a Jagla particle. Using discrete molecular dynamics, we calculate the thermodynamic properties of the resulting solutions. We systematically vary the set of parameters of the dimer and monomer models and find that one can readily reproduce the experimental behavior of the excess volume of the methanolwater system as a function of methanol volume fraction. We compare the pressure and temperature dependence of the excess volume and the excess enthalpy of both models with experimental data on methanol-water solutions and find qualitative agreement in most cases. We also investigate the solute effect on the temperature of maximum density and find that the effect of concentration isorders of magnitude stronger than measured experimentally.

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Modeling Amphiphilic Solutes in a Jagla Solvent

The influence of quantum bath effects on the dynamics of a quantum two-level system linearly coupled to a harmonic bath is studied when the coupling is both diagonal and off-diagonal. It is shown that the pure dephasing kernel and the non-adiabatic quantum transition rate between Born–Oppenheimer states of the subsystem can be decomposed into a contribution from thermally excited bath modes plus a zero point energy contribution. This quantum rate can be modewise factorized exactly into a product of a mixed quantum subsystem-classical bath transition rate and a quantum correction factor. This factor determines dynamics of quantum bath correlations. Quantum bath corrections to both the transition rate and the pure dephasing kernel are shown to be readily evaluated via a mixed quantum-classical simulation. Hence, quantum dynamics can be recovered from a mixed quantum-classical counterpart by incorporating the missing quantum bath corrections. Within a mixed quantum-classical framework, a simple approach for evaluating quantum bath corrections in calculation of the non-adiabatic transition rate is presented.

/pdf/constructing-quantum-dynamics-from-mixed-quantum-classical-4pid08n2yd.pdf

Constructing quantum dynamics from mixed quantum-classical descriptions

ordered, cylindrical conformations

Water. as we all know, has an essential role in living systems and is fundamentally involved in the structure and function of biological polymers, such as proteins. Because of the difficulties involved in theoretical studies of protein solutions per se. it is of interest to investigate those solvated systems of small molecules which incorporate functional groups present in proteins. In this paper, we describe the results of a molecular dynamics simulation of such a molecule, the alanine dipeptide in aqueous solution. In such a simulation, one treats a box of molecules of volume V with an energy and density corresponding to the system of interest. Given the internal and interaction potentials for the molecules in the box, and certain initial conditions for the coordinates and momenta of each particle, one solves the classical equations of motion for all the particles in order to obtain the phase space trajectory of the entire system over a period of time. An initial integration period during which certain properties (e.g., individual particle velocities) are adjusted is used to obtain an equilibrated system. After the equilibration period, integration is continued for a length of time sufficient to yield time averages that approximate equilibrium averages. In addition, the time evolution of particle trajectories can be used to determine time-dependen t properties. We examine structural, energetic, and dynamic aspects of both the dipeptide solute and the aqueous solvent. The details of the model used to simulate the dipeptide solution have been presented previously;’ a brief review of the interactions present in the system is given here. The alanine “dipeptide” solute (CH3C‘ONHCHCH,C‘ONHCH3] is a neutral molecule terminated by methyl groups, rather than by the carboxylic acid and amino groups of an amino acid. This is an appropriate choice to obtain a system that models an amino acid as part of a polypeptide chain. The geometry

Peter J. Rossky

Papers

A second-order Kubo response theory-centroid approach to vibrational energy relaxation for single-mode excitations

Modeling Amphiphilic Solutes in a Jagla Solvent

Constructing quantum dynamics from mixed quantum-classical descriptions

ordered, cylindrical conformations

Solvation of a dipeptide by water