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Science

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The Molecular Dynamics (MD) module of NWChem is designed for the simulation of biomolecular systems, with special features that facilitate the setup of complex systems such as memprane proteins embedded in complex microbial membranes consisting. These capabilities have been used to perform the first ever computer simulations of outer membrane proteins in lipopolysaccharide membranes, in a study of the [http://dx.doi.org/10.1002/prot.22165 OprF outer membrane protein of Pseudomonas aeruginosa.]
The Molecular Dynamics (MD) module of NWChem is designed for the simulation of biomolecular systems, with special features that facilitate the setup of complex systems such as memprane proteins embedded in complex microbial membranes consisting. These capabilities have been used to perform the first ever computer simulations of outer membrane proteins in lipopolysaccharide membranes, in a study of the [http://dx.doi.org/10.1002/prot.22165 OprF outer membrane protein of Pseudomonas aeruginosa.]
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=ECCE Graphical User Interface Provides End-to-End MD Support=
 
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[[File:Ecce.jpg|left|200px|Ecce’s end-to-end support for molecular dynamics calculations in NWChem greatly increases the ease of use.]]
 
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[http://ecce.pnl.gov/ ECCE] (Extensible Computational Chemistry Environment) 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.
 
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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. The next release will have the capability to build solid state materials and surfaces.
 

Revision as of 17:56, 27 January 2012

Contents

Science with NWChem

NWChem used by thousands of researchers 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. With NWChem, researchers can tackle molecular systems including biomolecules, nanostructures, actinide complexes, and materials. NWChem offers an extensive array of highly scalable, parallel 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 an extensive set of exchange-correlation functionals, time-dependent density functional theory (TDDFT), plane-wave DFT with exact exchange and Car-Parrinello, molecular dynamics with AMBER and CHARMM force fields, and combinations of them.

A list of research publications that utilized NWChem can be found here.

Ground State DFT Calculations

The local basis implementation of DFT in NWChem uses Gaussian atom centered Gaussian type orbitals (GTO) and can be used to study molecular, finite clusters and nanosystems. An exhaustive list of exchange-correlation functionals are supported including: traditional DFT, hybrid functionals, meta-type functionals, range-separated forms, double-hybrid functionals and dispersion corrections. All the available exchange-correlation functionals have associated analytic first derivatives and most functionals have associated second derivatives. Relativistic effects can also be included in DFT/HF calculations via the all-electron spin-free and spin–orbit one-electron Douglas–Kroll–Hess (DKH) method and zeroth-order relativistic approximation (ZORA) as well as through effective core (ECP) and spin–orbit (SO) potentials.

Excited State Calculations with TDDFT

TDDFT has become an attractive and efficient tool for reliable excited-state calculations involving single excitations in a wide range of systems spanning molecules to materials. However, a major drawback lies in the quality of the exchange-correlation functionals. It is well known that various commonly used functionals are reasonably accurate for valence excited states but fall short in the prediction of charge-transfer (CT) and Rydberg states. The recently developed range-separated functionals have been shown to be very encouraging for CT transitions and outperform their non-range-separated counterparts. Results with these functionals are also comparable with very high levels of theory like EOMCC. In addition to an exhaustive list of commonly used exchange-correlation functionals, several range-separated forms have been recently implemented and extensively validated in NWChem.

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.

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.

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 for comprehensive description of large molecular systems for chemistry and biology, including ground and excited state calculations, properties, efficient large scale optimizations, reaction pathways, dynamics, and free energy.

High Accuracy Is Achievable for Molecular Properties and Excited States

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

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. The LR-CCSD approach enables also highly-accurate estimates of the static hyperpolarizabilities for systems where low-rank methods fail.

Scalable Plane Wave Has Exact Exchange

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

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 and on iron-oxide surfaces as well as clay layers.

Molecular Dynamics of Complex Biomolecular Systems

Outer membrane OprF of Pseudomonas aeruginosa in a lipopolysaccharide membrane.

The Molecular Dynamics (MD) module of NWChem is designed for the simulation of biomolecular systems, with special features that facilitate the setup of complex systems such as memprane proteins embedded in complex microbial membranes consisting. These capabilities have been used to perform the first ever computer simulations of outer membrane proteins in lipopolysaccharide membranes, in a study of the OprF outer membrane protein of Pseudomonas aeruginosa.