NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Read the FAQ on how to use on the cluster.
Chemistry Simulation Software
VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.
NWChem is a computational chemistry package that is designed to run on high-performance parallel supercomputers as well as conventional workstation clusters.
You must setup the environment for nwchem first by creating a link to the NWChem config file:
ln -s /share/apps/simulations/nwchem-6.1.1/default.nwchemrc /home/username/.nwchemrc
Also read the FAQ on how to run NWChem on the cluster.
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.
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.
Please read our FAQ on running Siesta.
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.
Please read our FAQ on running ABINIT.
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.