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Software - Chemistry Simulation

ABINIT

ABINIT is used to find the total energy, charge density, and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a planewave or wavelet basis. Click here for information on running ABINIT.

Software Homepage: http://www.abinit.org/
Available on: Cheetah Cluster
Location: /share/apps/abinit


COLUMBUS

COLUMBUS is a collection of programs for high-level ab initio molecular electronic structure calculations. The programs are designed primarily for extended multi-reference (MR) calculations on electronic ground and excited states of atoms and molecules.

Software Homepage: http://www.univie.ac.at/columbus/
Available on: Cheetah Cluster
Location: /share/apps/Columbus


GAMESS

GAMESS (General Atomic and Molecular Electronic Structure System) is a program for ab initio molecular quantum chemistry. Click here for information on running GAMESS.

Software Homepage: http://www.msg.chem.iastate.edu/gamess/
Available on: Cheetah Cluster
Location: /share/apps/gamess


NAMD

NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Click here for information on running NAMD.

Software Homepage: http://www.ks.uiuc.edu/Research/namd/
Available on: Cheetah Cluster
Command: namd2
Location: /share/apps/namd


NWChem

NWChem is an open source computational chemistry package that is designed to run on high-performance parallel supercomputers as well as conventional workstation clusters. Click here for information on setting up and running NWChem.

Software Homepage: http://www.emsl.pnl.gov/docs/nwchem/nwchem.html
Available on: Cheetah Cluster
Command: nwchem
Location: /share/apps/simulations/nwchem-6.1.1/


Octopus

Octopus is a scientific program aimed at the ab initio virtual experimentation on a hopefully ever-increasing range of system types. Electrons are described quantum-mechanically within density-functional theory (DFT), in its time-dependent form (TDDFT) when doing simulations in time. Nuclei are described classically as point particles. Electron-nucleus interaction is described within the pseudopotential approximation.

Software Homepage: http://www.tddft.org/programs/octopus/wiki/index.php/Main_Page
Available on: Cheetah Cluster
Command: octopus
Location: /share/apps/octopus


SIESTA

SIESTA is both a method and its computer program implementation, to perform efficient electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids. Click here for information on running SIESTA.

Software Homepage: http://icmab.cat/leem/siesta/
Available on: Cheetah Cluster
Location: /share/apps/simulations/siesta-3.1/


VMD

VMD (Visual Molecular Dynamics) is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.

Software Homepage: http://www.ks.uiuc.edu/Research/vmd/
Available on: Linux workstations only
Command: VMD