modified on 1 September 2010 at 09:15 ••• 388,827 views

Science

From NWChem

Revision as of 09:15, 1 September 2010 by WikiSysop (Talk | contribs)
Jump to: navigation, search

NWChem enables researchers to run highly scalable, parallel computations on large, challenging scientific problems. Initially, the problems of interest were focused on environmental issues, but NWChem has recently been used to solve large scientific problems in many different areas, including the examination of metal clusters, biological systems, nanostructures, and materials.

With NWChem, researchers can tackle molecular systems including biomolecules, nanostructures,actinide complexes, and materials.

NWChem offers an extensive array of computational chemistry methods needed to address scientific questions that are relevant to reactive chemical processes occurring in our everyday environment—photosynthesis, protein functions, and combustion, to name a few. They include a multitude of highly correlated methods, density functional theory (DFT) with many exchange-correlation functionals, plane-wave DFT with exact exchange and Car-Parrinello, molecular dynamics with AMBER and CHARMM force fields, and combinations of them.

The NWChem computational chemistry software package runs large chemistry problems efficiently and is used by thousands of people worldwide to investigate questions about chemical processes by applying theoretical techniques to predict the structure, properties, and reactivity of chemical and biological species ranging in size from tens to millions of atoms.


Contents

High Accuracy Is Scalable to Large Problem Sizes

A comprehensive understanding of excited-state processes is crucial in many areas of chemistry, and NWChem has the methodologies capable of providing reliable characterization of excitation energies and excited-state potential energies. Several recent implementations based on the Equation-of-Motion Coupled Cluster (EOMCC) formalism offer a unique chance to address these problems. The largest up-to-date EOMCC calculations demonstrated that taking advantage of ever growing computer power the calculations with the EOMCC methodologies are possible for systems composed of 200-300 correlated electrons.

The EOMCC excitation energies for the oligoporphyrin dimer  are in a very good agreement with experimentally inferred values (J. Chem. Phys. 132, 154103 (2010)).
Highly correlated EOMCC methods accounting for higher-correlation effects can be used to describe electron transfer processes in challenging  open-shell systems (J.  Phys. Chem. A 114, 8764 (2010)).
New EOMCC formalisms can be also used to systems of biological relevance (β-carotene).


NWChem offers several variants of the EOMCC formalism – from rudimentary EOMCC model with singles and doubles (EOMCCSD) to more sophisticated methods accounting for the effect of triple excitations such as the non-iterative CR-EOMCCSD(T) method and the iterative EOMCCSDT approach and its active-space variant. These accurate formalisms can be used not only for calculations of vertical excitation energies but also to characterize excited-state potential energy surfaces. Various EOMCC approaches can be fully integrated with the multiscale approaches enabling the simulations of the excited-state processes in realistic settings. The correlated methodologies are utilized in this case as high-accuracy drivers for quantum part of the QM/MM and Embedded Clusters formalisms. This functionality provides a unique opportunity of excited-state studies of molecular systems in solution and localized excited states for materials. Another advantage of using TCE generated CC codes is a possibility of utilizing various types of reference functions for closed- and open-shell systems including RHF, ROHF, UHF, and DFT references. Recently developed solvers for the EOMCC theory enable one to deal with excited states of highly diversified configurational structure.

New EOMCC models for multiscale approaches  provide efficient tool for modeling excite states in true environment (Chem.Phys. Lett. 470, 353 (2009)).
Tensor Contraction Engine (TCE)  generated EOMCC codes can take advantage of massively parallel compute. The CR-EOMCCSD(T) implementation was shown to scale across 34,008 cores.

Extensive QM/MM Capabilities Are Seamlessly Integrated

The new QM/MM module provides a seamless integration between molecular mechanics and most quantum-mechanical theories in NWChem. It boasts an extensive array of capabilities geared toward comprehensive description of ground and excited state, and dynamical properties of large molecular systems for chemistry and biology. For example, QM/MM was used to model the catalytic properties in proteins.


Applying QM/MM: Modeling catalytic properties of protein kinases (left), and simulating reactions in aqueous solutions (right).


High Accuracy Is Achievable for Molecular Properties and Excited States

With the recently developed linear-response coupled-cluster module, high-precision calculations for static and dynamic molecular properties are possible. Several levels of theory have been implemented including models based on singles and doubles (LR-CCSD) as well as more sophisticated theories based on the singles, doubles, and triples (LR-CCSDT). The recent studies of static/dynamic polarizabilities for polyacenes and C60 molecule clearly demonstrate a great potential of the LR-CC theory in retaining the essential part of the correlation effects (J. Chem. Phys., 127, 144105 (2007); 129, 226101 (2008)). The LR-CCSD approach enables also highly-accurate estimates of the static hyperpolarizabilities for systems where low-rank methods fail (J. Chem. Phys. , 130, 194108 (2009)).


Excellent agreement between dipole polarizabilities of C60 calculated with NWChem using LR-CCSD and experimental values

Scalable Plane Wave Has Exact Exchange

The NWChem highly scalable Plane-Wave module now enables users to use exact exchange and the Self-Interaction Correction (SIC) within its framework for complex molecular, liquid, and solid-state systems. In addition, great improvements in parallel performance allow users to study larger systems at longer time scales with a faster time-to-solution. Scaling to 24,000 processors has been demonstrated for a 160 atom hematite cluster using density functional theory with exact exchange.

NWChem’s Car-Parrinello simulation capability, incorporating relativistic effects, was used to model the behavior of uranium in complex solution environments (J. Chem. Phys. 128, 124507, 2008) and on iron-oxide surfaces as well as clay layers.


Unique relativistic Car-Parrinello simulations uranyl in water show excellent agreement with available experimental data


Molecular Dynamics Allows Protons to Hop

The Molecular Dynamics (MD) module of NWChem now includes the capability for dynamic proton hopping using the new, efficient Q-HOP methodology developed by the Volkhard group at the University of Saarland, Germany. This technique relies on classical MD simulations in which stochastic instantaneous transfer between neighboring proton accepting groups is determined by an easily computable probability. This probability is based on a modified version of Transition State Theory incorporating tunneling at a semi-classical level.

MD simulations provide insight into why mutations in the active site of wild-type enzyme organophosphorous hydrolase result in a 4 orders-of-magnitude increase of catalytic activity

Ecce Graphical User Interface Provides End-to-End MD Support

The newest release of Ecce (Extensible Computational Chemistry Environment; version 4.0) provides full end-to-end support for the molecular dynamics module in NWChem. Through the graphical interface, users can set up their calculations, submit them to their computer platforms, and visualize the results on-the-fly.

Ecce provides an easy to use graphical user interface that enables novice users to set up quantum chemistry calculations, submit them on large supercomputers, and analyze and visualize the calculated data. Currently, the team is expanding its solid state capabilities.


Ecce’s end-to-end support for molecular dynamics calculations in NWChem greatly increases the ease of use.