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

/pdf/quantum-mechanical-continuum-solvation-models-3edv963g14.pdf

Quantum mechanical continuum solvation models.

ADVERTISEMENT RETURN TO ISSUEEditorialNEXTThe Age of Direct Chemical DynamicsJiali GaoJiali GaoShenzhen Bay LaboratoryUniversity of MinnesotaMore by Jiali Gaohttps://orcid.org/0000-0003-0106-7154 and Peter J. RosskyPeter J. RosskyRice UniversityMore by Peter J. Rosskyhttps://orcid.org/0000-0002-0461-4179Cite this: Acc. Chem. Res. 2022, 55, 4, 471–472Publication Date (Web):February 15, 2022Publication History Received11 January 2022Published online15 February 2022Published inissue 15 February 2022https://doi.org/10.1021/acs.accounts.2c00021Copyright © Published 2022 by American Chemical SocietyRIGHTS & PERMISSIONSArticle Views1691Altmetric-Citations-LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (497 KB) Get e-AlertscloseSUBJECTS:Chemical reactions,Direct dynamics,Excited states,Molecular dynamics,Molecular dynamics simulations Get e-Alerts 

https://pubs.acs.org/doi/pdf/10.1021/acs.accounts.2c00021

The Age of Direct Chemical Dynamics.

Molecular dynamics computer simulation is used to examine supercritical water's ability to solvate species of varying polarity along the reaction coordinate for the SN2 reaction of Cl- and CH3Cl at several conditions of density and temperature. At the critical temperature and reduced densities down to 0.5, the solute-solvent interactions are sufficiently strong to preserve solvent structure near the chloride ion with coordination numbers as high as in ambient water. We examine how these coordination numbers and the chloride-water hydrogen bonds eventually break down under extreme conditions of low densities and high temperatures.

Solvation of species of varying polarity in supercritical water: a computer simulation study

http://link.springer.com/content/pdf/10.1007/978-3-642-85176-6_199.pdf

Polarized Ultrafast Transient Spectroscopy of the Hydrated Electron: Quantum Non-Adiabatic Molecular-Dynamics Simulation

Molecular dynamics study of solvation in urea water solution

In order to develop a more complete understanding of the limitations of mixed quantum-classical simulation methods, the origins of electronic dephasing are analyzed in a simple model of the condensed phase, namely, the spin-boson model with an ohmic spectral density. We focus on the decay of the thermally averaged nuclear overlap/phase function ~NOPF!. Considering the strong coupling/high temperature limit, a relationship is obtained at short time between the rate of electronic coherence loss and the electronic dephasing rate characteristic of a classical bath. Using this relationship, we clarify the origin of the decay of the NOPF. In the same limit, we also reproduce an earlier relationship between the electronic decoherence time and a solvation relaxation time. Finally, we point out that, for the spin-boson model, the exact quantum mechanical description of electronic dephasing is reproduced by mixed quantum/classical methods if a Gaussian distribution of quantum fluctuations around each classical phase space point is introduced. That spatial distribution of quantum fluctuations is functionally the same as that appearing in the Feynman‐Kleinert variational local harmonic approximation, and also that implemented in existing classical trajectory-based estimates of coherence dissipation times. © 2004 American Institute of Physics. @DOI: 10.1063/1.1742979#

Peter J. Rossky

Papers

The Age of Direct Chemical Dynamics.

Solvation of species of varying polarity in supercritical water: a computer simulation study

Polarized Ultrafast Transient Spectroscopy of the Hydrated Electron: Quantum Non-Adiabatic Molecular-Dynamics Simulation

Molecular dynamics study of solvation in urea water solution

ARTICLES An analysis of electronic dephasing in the spin-boson model