Motivation: Molecular simulation has historically been a low-throughput technique, but faster computers and increasing amounts of genomic and structural data are changing this by enabling large-scale automated simulation of, for instance, many conformers or mutants of biomolecules with or without a range of ligands. At the same time, advances in performance and scaling now make it possible to model complex biomolecular interaction and function in a manner directly testable by experiment. These applications share a need for fast and efficient software that can be deployed on massive scale in clusters, web servers, distributed computing or cloud resources.

Results: Here, we present a range of new simulation algorithms and features developed during the past 4 years, leading up to the GROMACS 4.5 software package. The software now automatically handles wide classes of biomolecules, such as proteins, nucleic acids and lipids, and comes with all commonly used force fields for these molecules built-in. GROMACS supports several implicit solvent models, as well as new free-energy algorithms, and the software now uses multithreading for efficient parallelization even on low-end systems, including windows-based workstations. Together with hand-tuned assembly kernels and state-of-the-art parallelization, this provides extremely high performance and cost efficiency for high-throughput as well as massively parallel simulations.

Availability: GROMACS is an open source and free software available from http://www.gromacs.org.

Contact: erik.lindahl@scilifelab.se

Supplementary information:Supplementary data are available at Bioinformatics online.

Gromacs 4.5

The Avogadro project has developed an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible, high quality rendering, and a powerful plugin architecture. Typical uses include building molecular structures, formatting input files, and analyzing output of a wide variety of computational chemistry packages. By using the CML file format as its native document type, Avogadro seeks to enhance the semantic accessibility of chemical data types. The work presented here details the Avogadro library, which is a framework providing a code library and application programming interface (API) with three-dimensional visualization capabilities; and has direct applications to research and education in the fields of chemistry, physics, materials science, and biology. The Avogadro application provides a rich graphical interface using dynamically loaded plugins through the library itself. The application and library can each be extended by implementing a plugin module in C++ or Python to explore different visualization techniques, build/manipulate molecular structures, and interact with other programs. We describe some example extensions, one which uses a genetic algorithm to find stable crystal structures, and one which interfaces with the PackMol program to create packed, solvated structures for molecular dynamics simulations. The 1.0 release series of Avogadro is the main focus of the results discussed here. Avogadro offers a semantic chemical builder and platform for visualization and analysis. For users, it offers an easy-to-use builder, integrated support for downloading from common databases such as PubChem and the Protein Data Bank, extracting chemical data from a wide variety of formats, including computational chemistry output, and native, semantic support for the CML file format. For developers, it can be easily extended via a powerful plugin mechanism to support new features in organic chemistry, inorganic complexes, drug design, materials, biomolecules, and simulations. Avogadro is freely available under an open-source license from http://avogadro.openmolecules.net
 .

/pdf/avogadro-an-advanced-semantic-chemical-editor-visualization-2imnj3h9vl.pdf

Avogadro: an advanced semantic chemical editor, visualization, and analysis platform

A summary of the technical advances that are incorporated in the fourth major release of the Q-Chem quantum chemistry program is provided, covering approximately the last seven years. These include developments in density functional theory methods and algorithms, nuclear magnetic resonance (NMR) property evaluation, coupled cluster and perturbation theories, methods for electronically excited and open-shell species, tools for treating extended environments, algorithms for walking on potential surfaces, analysis tools, energy and electron transfer modelling, parallel computing capabilities, and graphical user interfaces. In addition, a selection of example case studies that illustrate these capabilities is given. These include extensive benchmarks of the comparative accuracy of modern density functionals for bonded and non-bonded interactions, tests of attenuated second order Moller–Plesset (MP2) methods for intermolecular interactions, a variety of parallel performance benchmarks, and tests of the accuracy of implicit solvation models. Some specific chemical examples include calculations on the strongly correlated Cr_2 dimer, exploring zeolite-catalysed ethane dehydrogenation, energy decomposition analysis of a charged ter-molecular complex arising from glycerol photoionisation, and natural transition orbitals for a Frenkel exciton state in a nine-unit model of a self-assembling nanotube.

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Advances in molecular quantum chemistry contained in the Q-Chem 4 program package

The Atomic Simulation Environment (ASE) is a software package written in the Python programming language with the aim of setting up, steering, and analyzing atomistic simula- tions. In ASE, tasks are fully scripted in Python. The powerful syntax of Python combined with the NumPy array library make it possible to perform very complex simulation tasks. For example, a sequence of calculations may be performed with the use of a simple "for-loop" construction. Calculations of energy, forces, stresses and other quantities are performed through interfaces to many external electronic structure codes or force fields using a uniform interface. On top of this calculator interface, ASE provides modules for performing many standard simulation tasks such as structure optimization, molecular dynamics, handling of constraints and performing nudged elastic band calculations.

/pdf/the-atomic-simulation-environment-a-python-library-for-48jb1pkf0e.pdf

The Atomic Simulation Environment - A Python library for working with atoms

A summary of the technical advances that are incorporated in the fourth major release of the Q-Chem quantum chemistry program is provided, covering approximately the last seven years. These include developments in density functional theory methods and algorithms, nuclear magnetic resonance (NMR) property evaluation, coupled cluster and perturbation theories, methods for electronically excited and open-shell species, tools for treating extended environments, algorithms for walking on potential surfaces, analysis tools, energy and electron transfer modelling, parallel computing capabilities, and graphical user interfaces. In addition, a selection of example case studies that illustrate these capabilities is given. These include extensive benchmarks of the comparative accuracy of modern density functionals for bonded and non-bonded interactions, tests of attenuated second order Møller–Plesset (MP2) methods for intermolecular interactions, a variety of parallel performance benchmarks, and tests of the accuracy of implicit solvation models. Some specific chemical examples include calculations on the strongly correlated Cr2 dimer, exploring zeolite-catalysed ethane dehydrogenation, energy decomposition analysis of a charged ter-molecular complex arising from glycerol photoionisation, and natural transition orbitals for a Frenkel exciton state in a nine-unit model of a self-assembling nanotube.

RESEARCH ARTICLE Advances in molecular quantum chemistry contained in the Q-Chem 4 program package

A PA5D (potential averaged 5D) TD (time-dependent) quantum wave-packet calculation is reported for the reaction D{sub 2} + OH {yields} D + DOH on the Schatz-Elgersma potential energy surface. The dynamics calculation is carried out on a workstation with a modest memory, which is made possible by using a normalized angular quadrature scheme to minimize the requirement for computer memory during wave-packet propagation. Reaction probabilities, cross sections, and rate constants are presented for the title reaction, and the comparison of the present result with those of the isotopic reactions, H{sub 2} + OH and HD + OH, is given. Consistent with its isotopic reactions, the rotational orientation of D{sub 2} has a stronger effect than that of OH and, in particular, the D{sub 2} (j=1) reactant produces the largest reaction probability, which is attributed to a general steric effect. The comparison of all three isotopic reactions shows that the reactivity (reaction probability and cross section) of the HH(D) + OH system is in the order of P{sub H(2)} > P{sub HD} > P{sub D(2)}. This trend is in good agreement with reduced dimensionality calculations. 27 refs., 8 figs., 4 tabs.

Quantum Dynamics Study for D2 + OH Reaction

An eight-degree-of-freedom (8DOF) time-dependent wave-packet approach has been developed to study the H2+C2H→H+C2H2 reaction system. The 8DOF model is obtained by fixing one of the Jacobi torsion angle in the nine-degree-of-freedom AB+CDE reaction system. This study is an extension of the previous seven-degree-of-freedom (7DOF) computation [J. Chem. Phys. 119, 12057 (2003)] of this reaction system. This study shows that vibrational excitations of H2 enhance the reaction probability, whereas the stretching vibrational excitations of C2H have only a small effect on the reactivity. Furthermore, the bending excitation of C2H, compared to the ground-state reaction probability, hinders the reactivity. A comparison of the rate constant between the 7DOF calculation and the present 8DOF results has been made. The theoretical and experimental results agree with each other very well when the present 8DOF results are adjusted to account for the lower transition state barrier heights found in recent ab initio calculat...

An eight-degree-of-freedom quantum dynamics study for the H2+C2H system.

Atomic-level, bimolecular nucleophilic substitution reaction mechanisms have been studied mostly in the gas phase, but the gas-phase results cannot be expected to reliably describe condensed-phase chemistry As a novel, double-inversion mechanism has just been found for the F− + CH3Cl SN2 reaction in the gas phase [Nat Commun, 2015, 6, 5972], here, using multi-level quantum mechanics methods combined with the molecular mechanics method, we discovered a new, double-inversion mechanism for this reaction in aqueous solution However, the structures of the stationary points along the reaction path show significant differences from those in the gas phase due to the strong influence of solvent and solute interactions, especially due to the hydrogen bonds formed between the solute and the solvent More importantly, the relationship between the two double-inversion transition states is not clear in the gas phase, but, here we revealed a novel intermediate complex serving as a “connecting link” between the two transition states of the abstraction-induced inversion and the Walden-inversion mechanisms A detailed reaction path was constructed to show the atomic-level evolution of this novel double reaction mechanism in aqueous solution The potentials of mean force were calculated and the obtained Walden-inversion barrier height agrees well with the available experimental value

A new, double-inversion mechanism of the F− + CH3Cl SN2 reaction in aqueous solution

The bimolecular nucleophilic substitution reaction of CCl4 and OH– in aqueous solution was investigated on the basis of a combined quantum mechanical and molecular mechanics method. A multilayered representation approach is employed to achieve high accuracy results at the CCSD(T) level of theory. The potential of mean force calculations at the DFT level and CCSD(T) level of theory yield reaction barrier heights of 22.7 and 27.9 kcal/mol, respectively. Both the solvation effects and the solvent-induced polarization effect have significant contributions to the reaction energetics, for example, the solvation effect raises the saddle point by 10.6 kcal/mol. The calculated rate constant coefficient is 8.6 × 10–28 cm3 molecule–1 s–1 at the standard state condition, which is about 17 orders magnitude smaller than that in the gas phase. Among the four chloromethanes (CH3Cl, CH2Cl2, CHCl3, and CCl4), CCl4 has the lowest free energy activation barrier for the reaction with OH– in aqueous solution, confirming the tr...

Hybrid Quantum Mechanical and Molecular Mechanics Study of the SN2 Reaction of CCl4+ OH-in Aqueous Solution: The Potential of Mean Force, Reaction Energetics, and Rate Constants

A time-dependent wave-packet approach is presented for the quantum dynamics study of the AB+CDE reaction system for zero total angular momentum. A seven-degree-of-freedom calculation is employed to study the chemical reaction of H2+C2H yields H + C2H2 by treating C2H as a linear molecule. Initial state selected reaction probabilities are presented for various initial ro-vibrational states. This study shows that vibrational excitation of H2 enhances the reaction probability, whereas the excitation of C2H has only a small effect on the reactivity. An integral cross section is also reported for the initial ground states of H2 and C2H. The theoretical and experimental results agree with each other very well when the calculated seven dimensional results are adjusted to account for the lower transition state barrier heights found in recent ab initio calculations.

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Dunyou Wang

Papers

Quantum Dynamics Study for D2 + OH Reaction

An eight-degree-of-freedom quantum dynamics study for the H2+C2H system.

A new, double-inversion mechanism of the F− + CH3Cl SN2 reaction in aqueous solution

Hybrid Quantum Mechanical and Molecular Mechanics Study of the SN2 Reaction of CCl4+ OH-in Aqueous Solution: The Potential of Mean Force, Reaction Energetics, and Rate Constants

Quantum Dynamics Scattering Study of AB+CDE Reactions: A Seven Dimensional Treatment for the H2+C2H Reaction