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

Multiwfn is a multifunctional program for wavefunction analysis. Its main functions are: (1) Calculating and visualizing real space function, such as electrostatic potential and electron localization function at point, in a line, in a plane or in a spatial scope. (2) Population analysis. (3) Bond order analysis. (4) Orbital composition analysis. (5) Plot density-of-states and spectrum. (6) Topology analysis for electron density. Some other useful utilities involved in quantum chemistry studies are also provided. The built-in graph module enables the results of wavefunction analysis to be plotted directly or exported to high-quality graphic file. The program interface is very user-friendly and suitable for both research and teaching purpose. The code of Multiwfn is substantially optimized and parallelized. Its efficiency is demonstrated to be significantly higher than related programs with the same functions. Five practical examples involving a wide variety of systems and analysis methods are given to illustrate the usefulness of Multiwfn. The program is free of charge and open-source. Its precompiled file and source codes are available from http://multiwfn.codeplex.com.

Multiwfn: a multifunctional wavefunction analyzer.

We report re-optimization of a recently proposed long-range corrected (LC) hybrid density functional [J.-D. Chai and M. Head-Gordon, J. Chem. Phys., 2008, 128, 084106] to include empirical atom–atom dispersion corrections. The resulting functional, ωB97X-D yields satisfactory accuracy for thermochemistry, kinetics, and non-covalent interactions. Tests show that for non-covalent systems, ωB97X-D shows slight improvement over other empirical dispersion-corrected density functionals, while for covalent systems and kinetics it performs noticeably better. Relative to our previous functionals, such as ωB97X, the new functional is significantly superior for non-bonded interactions, and very similar in performance for bonded interactions.

/pdf/long-range-corrected-hybrid-density-functionals-with-damped-44ti6za9f3.pdf

Long-range corrected hybrid density functionals with damped atom–atom dispersion corrections

CHARMM (Chemistry at HARvard Molecular Mechanics) is a highly versatile and widely used molecu- lar simulation program. It has been developed over the last three decades with a primary focus on molecules of bio- logical interest, including proteins, peptides, lipids, nucleic acids, carbohydrates, and small molecule ligands, as they occur in solution, crystals, and membrane environments. For the study of such systems, the program provides a large suite of computational tools that include numerous conformational and path sampling methods, free energy estima- tors, molecular minimization, dynamics, and analysis techniques, and model-building capabilities. The CHARMM program is applicable to problems involving a much broader class of many-particle systems. Calculations with CHARMM can be performed using a number of different energy functions and models, from mixed quantum mechanical-molecular mechanical force fields, to all-atom classical potential energy functions with explicit solvent and various boundary conditions, to implicit solvent and membrane models. The program has been ported to numer- ous platforms in both serial and parallel architectures. This article provides an overview of the program as it exists today with an emphasis on developments since the publication of the original CHARMM article in 1983.

/pdf/charmm-the-biomolecular-simulation-program-4kexem0xkx.pdf

CHARMM: the biomolecular simulation program.

Large-Scale Hybrid Density Functional Theory Calculations in the Condensed-Phase: \textit{Ab Initio} Molecular Dynamics in the Isobaric-Isothermal Ensemble

http://absimage.aps.org/image/MAR12/MWS_MAR12-2011-005206.pdf

The Role of Many-Body Dispersion Interactions in Molecular Crystal Polymorphism

http://absimage.aps.org/image/MAR14/MWS_MAR14-2013-005901.pdf

Van der Waals Interactions in Pyridine and Pyridine-like Molecular Crystals: An \textit{ab initio} Molecular Dynamics Study

The van der Waals (vdWs) forces between monolayers has been a unique distinguishing feature of exfoliable materials since the first isolation of graphene. However, the vdWs interaction of exfoliable materials with their substrates and how this interface force influences their interaction with the environment is yet to be well understood.Here, we experimentally and theoretically unravel the role of vdWs forces between the recently rediscovered wide band gap p-type vdW semiconductor violet phosphorus (VP), with various substrates (including, SiO$_2$, mica, Si, Au) and quantify how VP stability in air and its interaction with its surroundings is influenced by the interface force.Using a combination of infrared nanoimaging and theoretical modeling we find the vdWs force at the interface to be a main factor that influences how VP interacts with its surroundings.In addition, the hydrophobicity of the substrate and the substrate surface roughness modify the vdWs force there by influencing VP stability. Our results could guide in the selection of substrates when vdW materials are prepared and more generally highlight the key role of interface force effects that could significantly alter physical properties of vdWs materials.

Substrate Induced van der Waals Force Effect on the Stability of Violet Phosphorous

Ion-π interactions between the face of a molecular π-system and a cation or anion are among the strongest non-covalent interactions known, with applications throughout biochemistry and structural biology, molecular recognition and host-guest chemistry, as well as enzyme kinetics and organocatalysis. In this work, we examine the competing notions of selectivity and flexibility in this class of non-covalent interactions by investigating how certain π-systems can be promiscuous ion-π binders with the versatility to form favorable cation- and anion-π complexes. We focus our efforts on a detailed theoretical case study of the DNA/RNA nucleobases by first demonstrating that these π-systems are promiscuous ion-π binders with the biologically relevant Li+/Na+ cations and F-/Cl- anions via benchmark-quality quantum-mechanical binding energy curves computed at the CCSD(T)/CBS level of theory. Using a SAPT-based energy decomposition analysis, we explore the different physicochemical driving forces underlying the formation of cation- and anion-π complexes, as well as the crucial role played by charge penetration effects in determining the non-trivial (and often counterintuitive) electrostatics in anion-π systems. In doing so, a unified view of these rather distinct non-covalent binding motifs emerges with the finding that both cation- and anion-π complexes are strongly stabilized by an essentially ring-independent potential that can only be overcome by substantially unfavorable electrostatics. This work furnishes a more comprehensive explanation for decades of observed correlations between the equilibrium binding energy and the electrostatic potential above the ring, and provides new insight into the nature of selectivity and flexibility in this important class of non-covalent interactions. Quite interestingly, the analysis presented herein demonstrates that π-systems have an inherent propensity to bind both cations and anions, thereby implying that promiscuous ion-π binding is not an exotic property of the nucleobases and should be common in nature.

Robert A. DiStasio

Papers

Large-Scale Hybrid Density Functional Theory Calculations in the Condensed-Phase: \textit{Ab Initio} Molecular Dynamics in the Isobaric-Isothermal Ensemble

The Role of Many-Body Dispersion Interactions in Molecular Crystal Polymorphism

Van der Waals Interactions in Pyridine and Pyridine-like Molecular Crystals: An \textit{ab initio} Molecular Dynamics Study

Substrate Induced van der Waals Force Effect on the Stability of Violet Phosphorous

Attracting Opposites: Promiscuous Ion-π Binding in the DNA Nucleobases