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
 .

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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

The dynamics of the bimolecular nucleophilic substitution (SN2) reactions at nitrogen are less understood than those of their corresponding reactions at carbon. In this paper, we report an ab initio molecular dynamics approach to investigate the reaction mechanisms of the F- + NH2I SN2 reaction at nitrogen. We found not only the one-transition-state mechanisms, but also the composite mechanisms with two and three transition states. For the two-transition-state mechanisms, the double inversion mechanism and the proton-abstraction roundabout followed by the backside-attack reaction mechanism have been reported before; but we discovered that there is also a new, front-side attack followed by the backside-attack Walden-inversion mechanism. Furthermore, a composite mechanism with three transition states also shows up in the reactive trajectories. Our results show that, as the collision energy increases, the SN2 reactivity decreases, and the proton-abstraction reactivity increases. The two-transition-state mechanisms, especially the double-inversion mechanism, make the largest contribution to the SN2 reactivity, followed then by the one-transition-state mechanisms, with the three-transition-state mechanism contributing the least. The potential energy profiles of the reaction mechanisms are characterized at the CCSD(T)/aug-cc-pVTZ(PP) level of theory. The analysis on stationary points shows that the proton-abstraction inversion transition state is ∼12.4 kcal mol-1 lower than the Walden-inversion transition state in contrast to the corresponding reaction at carbon F- + CH3I, in which the former is ∼26.1 kcal mol-1 higher than the latter. This might explain why the composite mechanism of the double inversion mechanism contributes the most to the SN2 reactivity in the F- + NH2I reaction.

The importance of the composite mechanisms with two transition states in the F− + NH2I SN2 reaction

Time-dependent, quantum reaction dynamics wavepacket approach is employed to investigate the impacts of the translational, vibrational, and rotational motion on the HD +H3+ → H2D+ + H2 reaction using the Xie-Braams-Bowman potential energy surface [Z. Xie, B. J. Braams, and J. M. Bowman, J. Chem. Phys. 122, 224307 (2005)]10.1063/1.1927529. We treat this five atom reaction with a seven-degree-of-freedom model by fixing one Jacobi and one torsion angle related to H3+ at the lowest saddle point geometry of the potential energy surface. The initial state selected reaction probabilities show that the rotational excitations of H+-H2 greatly enhance the reactivity with the reaction probabilities increased double at high rotational states compared to the ground state. However, the vibrational excitations of H3+ hinder the reactivity. The ground state reaction probability shows no reaction threshold for this exoergic reaction, and as the translational energy increases, the reaction probability decreases. Furthermor...

A quantum reaction dynamics study of the translational, vibrational, and rotational motion effects on the HD + H3+ reaction.

Eight-dimensional, quantum reaction dynamics, study of the isotopic reaction D2 + C2H

We employ a multilevel quantum mechanics and molecular mechanics method to investigate the double-inversion mechanism of the nucleophilic substitution reaction at the N center: the F- + NH2Cl reaction in aqueous solution. We find that the structures of the stationary points along the reaction path are quite different from the ones in the gas phase owing to the hydrogen-bond interactions between the solute and the surrounding water molecules. The atomic-level evolutions of the structures and charge transfer along the reaction path show that this double-inversion mechanism consists of an upside-down proton inversion process and a Walden-inversion process. The computed potential of mean force at the coupled-cluster singles and doubles with perturbative triples (CCSD(T))/molecular mechanics (MM) level of theory has the two-inversion barrier heights, and reaction free energy at 11.7, 29.6, and 12.6 kcal/mol, agreeing well with the predicted ones at 12.6, 32.5, and 12.2 kcal/mol obtained on the basis of the gas-phase reaction path and the solvation free energies of the stationary points.

Dunyou Wang

Papers

The importance of the composite mechanisms with two transition states in the F− + NH2I SN2 reaction

A quantum reaction dynamics study of the translational, vibrational, and rotational motion effects on the HD + H3+ reaction.

Eight-dimensional, quantum reaction dynamics, study of the isotopic reaction D2 + C2H

Multilevel Quantum Mechanics and Molecular Mechanics Study of the Double-Inversion Mechanism at Nitrogen: F– + NH2Cl in Aqueous Solution

Quantum dynamics study of energy efficiency on reactivity for the double-barrier potential energy surface of the N + N2 reaction