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Capabilities

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=Functionality=
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=Comprehensive Suite of Scalable Capabilities=
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NWChem provides many methods to compute the properties of molecular and periodic systems using standard quantum mechanical descriptions of the electronic wavefunction or density. In addition, NWChem has the capability to perform classical molecular dynamics and free energy simulations. These approaches may be combined to perform mixed quantum-mechanics and molecular-mechanics simulations.
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NWChem provides many methods for computing the properties of molecular and periodic systems using standard quantum mechanical descriptions of the electronic wavefunction or density. Its classical molecular dynamics capabilities provide for the simulation of macromolecules and solutions, including the computation of free energies using a variety of force fields. These approaches may be combined to perform mixed quantum-mechanics and molecular-mechanics simulations.  
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NWChem is available on almost all high performance computing platforms, workstations, PCs running LINUX, as well as clusters of desktop platforms or workgroup servers. NWChem development has been devoted to providing maximum efficiency on massively parallel processors. It achieves this performance on the 1960 processors HP Itanium2 system in the EMSL's MSCF. It has not been optimized for high performance on single processor desktop systems.
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The specific methods for determining molecular electronic structure, molecular dynamics, and pseudopotential plane-wave electronic structure and related attributes are listed in the following sections.
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==Molecular electronic structure==
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==Molecular Electronic Structure==
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The following quantum mechanical methods are available to calculate energies, analytic first derivatives and second derivatives with respect to atomic coordinates.
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Methods for determining energies and analytic first derivatives with respect to atomic coordinates include the following:
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* Self Consistent Field (SCF) or Hartree Fock (RHF, UHF).
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Hartree-Fock (RHF, UHF, high-spin ROHF)
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* Gaussian Density Functional Theory (DFT), using many local, non-local (gradient-corrected), and hybrid (local, non-local, and HF) exchange-correlation potentials (spin-restricted) with formal <math>N^3</math> and <math>N^4</math> scaling.
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Gaussian orbital-based density functional theory (DFT) using many local and non-local exchange-correlation potentials (LDA, LSDA)
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• second-order perturbation theory (MP2) with RHF and UHF references
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• complete active space self-consistent field theory (CASSCF).
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The following methods are available to calculate energies and analytic first derivatives with respect to atomic coordinates. Second derivatives are computed by finite difference of the first derivatives.
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Analytic second derivatives with respect to atomic coordinates are available for RHF and UHF, and closed-shell DFT with all functionals.
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* Self Consistent Field (SCF) or Hartree Fock (ROHF).
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The following methods are available to compute energies only:
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* Gaussian Density Functional Theory (DFT), using many local, non-local (gradient-corrected), and hybrid (local, non-local, and HF) exchange-correlation potentials (spin-unrestricted) with formal <math>N^3</math> and <math>N^4</math> scaling.
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* Spin-orbit DFT (SODFT), using many local and non-local (gradient-corrected) exchange-correlation potentials (spin-unrestricted).
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* MP2 including semi-direct using frozen core and RHF and UHF reference.
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* Complete active space SCF (CASSCF).
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The following methods are available to compute energies only. First and second derivatives are computed by finite difference of the energies.
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• iterative CCSD, CCSDT, and CCSDTQ methods and their EOM-CC counterparts for RHF, ROHF, and UHF references
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• active-space CCSDt and EOM-CCSDt approaches
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• completely renormalized CR-CCSD(T), and CR-EOM-CCSD(T) correction to EOM-CCSD excitation energies
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• locally renormalized CCSD(T) and CCSD(TQ) approaches
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• non-iterative approaches based on similarity transformed Hamiltonian: the CCSD(2)T and  CCSD(2) formalisms.
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• MP2 with RHF reference and resolution of the identity integral approximation MP2 (RI-MP2) with RHF and UHF references
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• selected CI with second-order perturbation correction.
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* CCSD, CCSD(T), CCSD+T(CCSD), with RHF reference.
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For all methods, the following may be performed:
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* Selected-CI with second-order perturbation correction.
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* MP2 fully-direct with RHF reference.
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* Resolution of the identity integral approximation MP2 (RI-MP2), with RHF and UHF reference.
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* CIS, TDHF, TDDFT, and Tamm-Dancoff TDDFT for excited states with RHF, UHF, RDFT, or UDFT reference.
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* CCSD(T) and CCSD[T] for closed- and open-shell systems (TCE module)
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* UCCD, ULCCD, UCCSD, ULCCSD, UQCISD, UCCSDT, and UCCSDTQ with RHF, UHF, or ROHF reference.
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* UCISD, UCISDT, and UCISDTQ with RHF, UHF, or ROHF reference.
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* Non-canonical UMP2, UMP3, and UMP4 with RHF or UHF reference.
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* EOM-CCSD, EOM-CCSDT, EOM-CCSDTQ for excitation energies, transition moments, and excited-state dipole moments of closed- and open-shell systems
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* CCSD, CCSDT, CCSDTQ for dipole moments of closed- and open-shell systems
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For all methods, the following operations may be performed:
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• single point energy calculations
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• geometry optimization with constraints (minimization and transition state)
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• molecular dynamics on the fully ab initio potential energy surface
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• automatic computation of numerical first and second derivatives
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• normal mode vibrational analysis in Cartesian coordinates
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• ONIOM hybrid calculations
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• Conductor-Like Screening Model (COSMO) calculations
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• electrostatic potential from fit of atomic partial charges
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• spin-free one-electron Douglas-Kroll calculations
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• electron transfer (ET)
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• vibrational SCF and DFT.
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* Single point energy
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At the SCF and DFT level of theory various (response) properties are available, including NMR shielding tensors and indirect spin-spin coupling.
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* Geometry optimization (minimization and transition state)
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* Molecular dynamics on the fully ab initio potential energy surface
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* Numerical first and second derivatives automatically computed if analytic derivatives are not available
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* Normal mode vibrational analysis in cartesian coordinates
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* ONIOM hybrid method of Morokuma and co-workers
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* Generation of the electron density file for graphical display
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* Evaluation of static, one-electron properties.
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* Electrostatic potential fit of atomic partial charges (CHELPG method with optional RESP restraints or charge constraints)
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For closed and open shell SCF and DFT:
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==Quantum Mechanics/Molecular Mechanics (QM/MM)==
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* COSMO energies - the continuum solvation `COnductor-like Screening MOdel' of A. Klamt and G. Sch&uuml;&uuml;rmann to describe dielectric screening effects in solvents.
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The QM/MM module in NWChem provides a comprehensive set of capabilities to study ground and excited state properties of large-molecular systems. The QM/MM module can be used with practically any quantum mechanical method available in NWChem. The following tasks are supported
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In addition, automatic interfaces are provided to
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• single point energy and property calculations
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• excited states calculation
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• optimizations and transition state search
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• dynamics
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• free energy calculations.
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* Python
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==Pseudopotential Plane-Wave Electronic Structure==
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* the POLYRATE direct dynamics software
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==Relativistic effects==
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The NWChem Plane-Wave (NWPW) module uses pseudopotentials and plane-wave basis sets to perform DFT calculations. This method's efficiency and accuracy make it a desirable first principles method of simulation in the study of complex molecular, liquid, and solid-state systems. Applications for this first principles method include the calculation of free energies, search for global minima, explicit simulation of solvated molecules, and simulations of complex vibrational modes that cannot be described within the harmonic approximation.
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The following methods for including relativity in quantum chemistry calculations are available:
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The NWPW module is a collection of three modules:  
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* Spin-free and spin-orbit one-electron Douglas-Kroll and zeroth-order regular approximations (ZORA) are available for all quantum mechanical methods and their gradients.
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• PSPW (PSeudopotential Plane-Wave) A gamma point code for calculating molecules, liquids, crystals, and surfaces.  
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* Dyall's spin-free Modified Dirac Hamiltonian approximation is available for the Hartree-Fock method and its gradients.
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• Band  A band structure code for calculating crystals and surfaces with small band gaps (e.g. semi-conductors and metals).  
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* One-electron spin-orbit effects can be included via spin-orbit potentials. This option is available for DFT and its gradients, but has to be run without symmetry.
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• PAW (Projector Augmented Wave) a gamma point projector augmented plane-wave code for calculating molecules, crystals, and surfaces.
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==Pseudopotential plane-wave electronic structure==
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These capabilities are available:
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Two modules are available to compute the energy, optimize the geometry, numerical second derivatives, and perform ab initio molecular dynamics using pseudopotential plane-wave DFT.
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• constant energy and constant temperature Car-Parrinello molecular dynamics (extended Lagrangian dynamics)
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• LDA, PBE96, and PBE0, exchange-correlation potentials (restricted and unrestricted)
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• SIC, pert-OEP, Hartree-Fock, and hybrid functionals (restricted and unrestricted)
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• Hamann, Troullier-Martins, Hartwigsen-Goedecker-Hutter norm-conserving pseudopotentials with semicore corrections
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• geometry/unit cell optimization, frequency, transition-states
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• fractional occupation of molecular orbitals for metals
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• AIMD/MM capability in PSPW
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• constraints needed for potential of mean force (PMF) calculation
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• wavefunction, density, electrostatic, Wannier plotting
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• band structure and density of states generation
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* PSPW - (Pseudopotential plane-wave) A gamma point code for calculating molecules, liquids, crystals, and surfaces.
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==Molecular Dynamics==
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* Band - A prototype band structure code for calculating crystals and surfaces with small band gaps (e.g. semi-conductors and metals)
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With
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The NWChem Molecular Dynamics (MD) module can perform classical simulations using the AMBER and CHARMM force fields, quantum dynamical simulations using any of the quantum mechanical methods capable of returning gradients, and mixed quantum mechanics molecular dynamics simulation and molecular mechanics energy minimization.
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* Conjugate gradient and limited memory BFGS minimization
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Classical molecular simulation functionality includes the following methods:
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* Car-Parrinello (extended Lagrangian dynamics)
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* Constant energy and constant temperature Car-Parrinello simulations
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* Fixed atoms in cartesian and SHAKE constraints in Car-Parrinello
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* Pseudopotential libraries
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* Hamann and Troullier-Martins norm-conserving pseudopotentials with optional semicore corrections
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* Automated wavefunction initial guess, now with LCAO
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* Vosko and PBE96 exchange-correlation potentials (spin-restricted and unrestricted)
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* Orthorhombic simulation cells with periodic and free space boundary conditions.
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* Modules to convert between small and large plane-wave expansions
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* Interface to DRIVER, STEPPER, and VIB modules
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* Polarization through the use of point charges
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* Mulliken, point charge, DPLOT (wavefunction, density and electrostatic potential plotting) analysis
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==Molecular dynamics==
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• single configuration energy evaluation
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• energy minimization
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• molecular dynamics simulation
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• free energy simulation (MCTI and MSTP with single or dual topologies, double-wide sampling, and separation-shifted scaling).
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The following functionality is available for classical molecular simulations:
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The classical force field includes the following elements:
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* Single configuration energy evaluation
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• effective pair potentials
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* Energy minimization
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• first-order polarization
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* Molecular dynamics simulation
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• self-consistent polarization
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* Free energy simulation (multistep thermodynamic perturbation (MSTP) or multiconfiguration thermodynamic integration (MCTI) methods with options of single and/or dual topologies, double wide sampling, and separation-shifted scaling)
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• smooth particle mesh Ewald
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• twin-range energy and force evaluation
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The classical force field includes:
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• periodic boundary conditions
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SHAKE constraints
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* Effective pair potentials (functional form used in AMBER, GROMOS, CHARMM, etc.)
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• constant temperature and/or pressure ensembles
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* First order polarization
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• dynamic proton hopping using the Q-HOP methodology
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* Self consistent polarization
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• advanced system setup capabilities for biomolecular membranes.
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* Smooth particle mesh Ewald (SPME)
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* Twin range energy and force evaluation
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* Periodic boundary conditions
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* SHAKE constraints
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* Consistent temperature and/or pressure ensembles
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NWChem also has the capability to combine classical and quantum descriptions in order to perform:
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* Mixed quantum-mechanics and molecular-mechanics (QM/MM) minimizations and molecular dynamics simulation , and
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* Quantum molecular dynamics simulation by using any of the quantum mechanical methods capable of returning gradients.
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By using the DIRDYVTST module of NWChem, the user can write an input file to the POLYRATE program, which can be used to calculate rate constants including quantum mechanical vibrational energies and tunneling contributions.
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==Python==
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The Python programming language has been embedded within NWChem and many of the high level capabilities of NWChem can be easily combined and controlled by the user to perform complex operations.
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==Parallel tools and libraries (Global Arrays Toolkit)==
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* Global arrays (GA)
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* Agregate Remote Memory Copy Interface (ARMCI)
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* Linear Algebra (PeIGS) and FFT
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* ParIO
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* Memory allocation (MA)
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Revision as of 12:14, 31 August 2010

Contents

Comprehensive Suite of Scalable Capabilities

NWChem provides many methods for computing the properties of molecular and periodic systems using standard quantum mechanical descriptions of the electronic wavefunction or density. Its classical molecular dynamics capabilities provide for the simulation of macromolecules and solutions, including the computation of free energies using a variety of force fields. These approaches may be combined to perform mixed quantum-mechanics and molecular-mechanics simulations.

The specific methods for determining molecular electronic structure, molecular dynamics, and pseudopotential plane-wave electronic structure and related attributes are listed in the following sections.

Molecular Electronic Structure

Methods for determining energies and analytic first derivatives with respect to atomic coordinates include the following:

• Hartree-Fock (RHF, UHF, high-spin ROHF) • Gaussian orbital-based density functional theory (DFT) using many local and non-local exchange-correlation potentials (LDA, LSDA) • second-order perturbation theory (MP2) with RHF and UHF references • complete active space self-consistent field theory (CASSCF).

Analytic second derivatives with respect to atomic coordinates are available for RHF and UHF, and closed-shell DFT with all functionals.

The following methods are available to compute energies only:

• iterative CCSD, CCSDT, and CCSDTQ methods and their EOM-CC counterparts for RHF, ROHF, and UHF references • active-space CCSDt and EOM-CCSDt approaches • completely renormalized CR-CCSD(T), and CR-EOM-CCSD(T) correction to EOM-CCSD excitation energies • locally renormalized CCSD(T) and CCSD(TQ) approaches • non-iterative approaches based on similarity transformed Hamiltonian: the CCSD(2)T and CCSD(2) formalisms. • MP2 with RHF reference and resolution of the identity integral approximation MP2 (RI-MP2) with RHF and UHF references • selected CI with second-order perturbation correction.

For all methods, the following may be performed:

• single point energy calculations • geometry optimization with constraints (minimization and transition state) • molecular dynamics on the fully ab initio potential energy surface • automatic computation of numerical first and second derivatives • normal mode vibrational analysis in Cartesian coordinates • ONIOM hybrid calculations • Conductor-Like Screening Model (COSMO) calculations • electrostatic potential from fit of atomic partial charges • spin-free one-electron Douglas-Kroll calculations • electron transfer (ET) • vibrational SCF and DFT.

At the SCF and DFT level of theory various (response) properties are available, including NMR shielding tensors and indirect spin-spin coupling.

Quantum Mechanics/Molecular Mechanics (QM/MM)

The QM/MM module in NWChem provides a comprehensive set of capabilities to study ground and excited state properties of large-molecular systems. The QM/MM module can be used with practically any quantum mechanical method available in NWChem. The following tasks are supported

• single point energy and property calculations • excited states calculation • optimizations and transition state search • dynamics • free energy calculations.

Pseudopotential Plane-Wave Electronic Structure

The NWChem Plane-Wave (NWPW) module uses pseudopotentials and plane-wave basis sets to perform DFT calculations. This method's efficiency and accuracy make it a desirable first principles method of simulation in the study of complex molecular, liquid, and solid-state systems. Applications for this first principles method include the calculation of free energies, search for global minima, explicit simulation of solvated molecules, and simulations of complex vibrational modes that cannot be described within the harmonic approximation.

The NWPW module is a collection of three modules:

• PSPW (PSeudopotential Plane-Wave) A gamma point code for calculating molecules, liquids, crystals, and surfaces. • Band A band structure code for calculating crystals and surfaces with small band gaps (e.g. semi-conductors and metals). • PAW (Projector Augmented Wave) a gamma point projector augmented plane-wave code for calculating molecules, crystals, and surfaces.

These capabilities are available:

• constant energy and constant temperature Car-Parrinello molecular dynamics (extended Lagrangian dynamics) • LDA, PBE96, and PBE0, exchange-correlation potentials (restricted and unrestricted) • SIC, pert-OEP, Hartree-Fock, and hybrid functionals (restricted and unrestricted) • Hamann, Troullier-Martins, Hartwigsen-Goedecker-Hutter norm-conserving pseudopotentials with semicore corrections • geometry/unit cell optimization, frequency, transition-states • fractional occupation of molecular orbitals for metals • AIMD/MM capability in PSPW • constraints needed for potential of mean force (PMF) calculation • wavefunction, density, electrostatic, Wannier plotting • band structure and density of states generation

Molecular Dynamics

The NWChem Molecular Dynamics (MD) module can perform classical simulations using the AMBER and CHARMM force fields, quantum dynamical simulations using any of the quantum mechanical methods capable of returning gradients, and mixed quantum mechanics molecular dynamics simulation and molecular mechanics energy minimization.

Classical molecular simulation functionality includes the following methods:

• single configuration energy evaluation • energy minimization • molecular dynamics simulation • free energy simulation (MCTI and MSTP with single or dual topologies, double-wide sampling, and separation-shifted scaling).

The classical force field includes the following elements:

• effective pair potentials • first-order polarization • self-consistent polarization • smooth particle mesh Ewald • twin-range energy and force evaluation • periodic boundary conditions • SHAKE constraints • constant temperature and/or pressure ensembles • dynamic proton hopping using the Q-HOP methodology • advanced system setup capabilities for biomolecular membranes.