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

We investigate the bimolecular nucleophilic substitution (SN2) reaction of F- with CH3CH2Cl in aqueous solution using combined multilevel quantum mechanism (ML-QM) theories with molecular mechanics (MM). The synchronized, atomic-level structural and charge evolutions are analyzed along the reaction path. The potential mean force along the reaction path in water is calculated at high-accuracy CCSD(T)/aug-cc-pVTZ/MM level of theory with a free energy barrier of 16.8 kcal/mol and a free energy of reaction of -9.7 kcal/mol. The water solvent hinders the reactivity by raising its reaction barrier by 15.1 kcal/mol, of which 13.6 kcal/mol comes from solvent energy contribution and 1.5 kcal/mol comes from the polarization effect. This indicates that the water solvent plays an essential role on this reaction in aqueous solution. We also predict the potential mean force profile based on the gas-phase reaction path and the solvation free energies of the stationary points; the comparison between our calculated result at CCSD(T)/MM level shows an excellent agreement with the predicted one with the free energy barrier at 16.2 kcal/mol and the free energy of reaction at -8.3 kcal/mol.

Atomic-Level Mechanism, Solvent Effect, and Potential of the Mean Force of the F- + CH3CH2Cl SN2 Reaction in Aqueous Solution.

1OH reaction and produces two distinguishable products–HOH and HOD. In order to make the TD calculation possible on workstations with limitedmemories, we employed a normalized quadrature scheme in the wavepacket propagation by thesplit-operator propagator. The normalized quadrature scheme eliminates the need to store largematrices during the wavepacket propagation while preserving the unitarity of the split-operatorpropagator and producing numerically stable results. This approach made TD dynamics calculationspossible on small-memory workstations for the title reaction and for other polyatomic reactions.Reaction probabilities, cross sections, rate constants, and reaction branching ratios are reported inthis paper for the title reaction. The observed strong dependence of the reaction probabilities on thereactive HD rotation and the relative weak dependence on the nonreactive OH rotation are explainedin terms of a steric effect. The isotope effect in the branching ratio is examined and physicalexplanation is given for the observed branching ratio at low and high kinetic energies. © 1995American Institute of Physics.

Quantum dynamics study of the reaction HD1OHòH1DOH, D1HOH

Rich reactive resonances are found in a 3D quantum dynamics study of the N + N2 exchange reaction using a recently developed ab initio potential energy surface. This surface is characterized by a feature in the interaction region called Lake Eyring , that is, two symmetric transition states with a shallow minimum between them. An L2 analysis of the quasibound states associated with the shallow minimum confirms that the quasibound states associated with oscillations in all three degrees of freedom in Lake Eyring are responsible for the reactive resonances in the state-to-state reaction probabilities. The quasibound states, mostly the bending motions, give rise to strong reasonance peaks, whereas other motions contribute to the bumps and shoulders in the resonance structure. The initial state reaction probability further proves that the bending motions are the dominating factors of the reaction probability and have longer life times than the stretching motions. This is the first observation of reactive resonances from a "Lake Eyring" feature in a potential energy surface.

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Reactive Resonances in N+N2 Exchange Reaction

The effects of proportion and location of pyrimidinyl for modulation of rectification on the structure of quaterphenyl

Ab initio molecular dynamics calculations were performed to study H2 dissociation mechanisms on Cu13 and defective graphene-supported Cu13 clusters. The study reveals that seven types of corresponding dissociation processes are found on the two clusters. The average dissociation energy barriers are 0.51 eV on the Cu13 cluster and 0.12 eV on the defective graphene-supported Cu13 cluster, which are lowered by ~ 19% and ~ 81% compared with the pristine Cu(111) surface, respectively. Furthermore, compared with the pure Cu13 cluster, the average dissociation energy barrier on the defective graphene-supported Cu13 cluster is substantially reduced by about 76%. The preferred dissociation mechanisms on the two clusters are H2 located at a top-bridge site with the barrier heights of 0.30 eV on the Cu13 cluster and - 0.31 eV on the defective graphene-supported Cu13 cluster. Analysis of the H-Cu bond interactions in the transition states shows that the antibonding-orbital center shifts upwards on the defective graphene-supported Cu13 cluster compared with the one on the Cu13 cluster, which explains the reduction of the dissociation energy barrier. The average adsorption energy of dissociated H atoms is also greatly enhanced on the defective graphene-supported Cu13 cluster, about twice that on pure Cu13.

Ab initio molecular dynamics study of H2 dissociation mechanisms on Cu13 and defective graphene-supported Cu13 clusters: active sites, energy barriers and adsorption states.

Dunyou Wang

Papers

Atomic-Level Mechanism, Solvent Effect, and Potential of the Mean Force of the F- + CH3CH2Cl SN2 Reaction in Aqueous Solution.

Quantum dynamics study of the reaction HD1OHòH1DOH, D1HOH

Reactive Resonances in N+N2 Exchange Reaction

The effects of proportion and location of pyrimidinyl for modulation of rectification on the structure of quaterphenyl

Ab initio molecular dynamics study of H2 dissociation mechanisms on Cu13 and defective graphene-supported Cu13 clusters: active sites, energy barriers and adsorption states.