Computational Chemistry Software at TACC and The GridChem Computational Chemistry Grid

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Computational Chemistry Software at TACC and
The GridChem Computational Chemistry Grid

• Dr. Chona S. Guiang
• April 2, 2007

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Outline

• Computational chemistry
• 1.1 Quantum chemistry
• 1.2. Molecular modeling
• Quantum chemistry software
• 2.1. NWChem
• 2.2. GAMESS
• Molecular modeling software
• 3.1. Gromacs
• 3.2. NAMD
• 3.3. Amber
• The Computational Chemistry Grid

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Computational chemistry

• Spans a broad range of spatial scales from
  electrons to atoms/molecules to continuous
  materials
• Spans a broad range of temporal scales from
  femtoseconds to microseconds
• Multi-scale treatment of time and spatial scales
  necessitate different theoretical treatments
• Multi-disciplinary in nature and scope

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Two broad categories

• Quantum chemistry
• Involves solving the Schroedinger equation
• Simplest approximation is Hartree-Fock. At this
  level, the electronic repulsion is replaced by an
  average potential
• Electron correlation can be computed to refine
  the HF calculation

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Two broad categories

• 2. Molecular modeling
• Concerned with atoms/molecular calculations
• Simplest approximation is molecular mechanics
  which uses classical treatment of internal
  molecular degrees of freedom
• Molecular dynamics integrates Newtons laws of
  motion to calculate the trajecory of molecular
  systems

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Quantum chemistry software

• GAMESS General Atomic and Molecular Electronic
  Structure System
• Properties calculated energies, forces,
  vibrational frequencies, multipoles, IR and Raman
  intensities
• SCF wave functions ranging from RHF, ROHF, UHF,
  GVB, and MCSCF
• Post SCF/HF CI, MP2, Coupled-Cluster approaches,
  DFT
• Installed on lonestar and champion

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Quantum chemistry software

• 2. NWChem
• Properties calculated energies, forces,
  vibrational frequencies, single atom charges
• SCF wave functions ranging from RHF, ROHF, UHF,
  GVB, and MCSCF
• Post SCF CI, MP2, Coupled-Cluster approaches,
  DFT, CASSCF
• Quantum dynamics
• Car-Parinello
• Molecular dynamics (force field includes AMBER,
  GROMOS, CHARMM)
• Coupled QM/MM dynamics
• Installed on lonestar and champion

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Molecular modeling software

• Gromacs
• Performs MD calculations
• Force field GROMOS-96
• Temperature and pressure coupling
• Constraint dynamics
• Long-range electrostatics using Ewald summation
• Energy minimization
• Normal mode analysis
• Free energy calculations
• Replica exchange
• coupled QM/MM dynamics
• Installed on lonestar only

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Molecular modeling software

• 2. NAMD
• Performs MD calculations
• Force field CHARMM19, CHARMM22, CHARMM27, Amber,
  OPLS, Gromacs
• Temperature and pressure coupling
• Constraint dynamics
• Long-range electrostatics using Ewald summation
• Energy minimization
• Normal mode analysis
• Free energy calculations
• Replica exchange
• Interactive steering with VMD
• Installed on lonestar only

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Molecular modeling software

• 3. Amber
• Performs MD calculations
• Force field Amber, F99, FF02, FF03, Amoeba
• Temperature and pressure coupling
• Constraint dynamics
• Long-range electrostatics using Ewald summation
• Energy minimization
• Normal mode analysis
• Free energy calculations
• Replica exchange
• Coupled QM/MM dynamics
• path integral MD
• Installed on lonestar and champion

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Using chemistry software at TACC

• Load application module file to configure correct
  runtime environment
• lonestar module load namd
• Use module help for more information on what the
  module file does
• lonestar module help namd
• Invoke program as you would any parallel program
• lonestar ibrun args

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GridChem demo

• (if time permits)

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References

• GAMESS http//www.msg.ameslab.gov/GAMESS/
• NWChem http//www.emsl.pnl.gov/docs/nwchem/nwchem.
  html
• Gromacs http//www.gromacs.org/
• NAMD http//www.ks.uiuc.edu/Research/namd/
• Amber http//amber.scripps.edu/
• GridChem www.gridchem.org