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This page is intended to serve as a community and information hub for our computational chemistry, biochemistry and biophysics (condense matter physics and chemistry) users. It is our hope that users and staff who are chemistry and biosystems savvy will be able to share tips and tricks, information about what their groups are doing, and knowledge about the various computational packages available.

Please do edit this page and/or create sub-pages. We ask that information is entered in the wiki (as opposed to linked from a third-party) as much as possible in order to retain the benefits of collective authorship. Remember to tag sub-pages with the category Chemistry, BioChemistry and Biophysics.


Computational chemistry is a branch of chemistry that incorporates the results of theoretical chemistry into efficient computer programs to calculate the structures and properties of molecules and solids. Various methods can be used to calculate properties such as structure, absolute and relative energies, electronic charge distributions, dipoles and higher multipole moments, vibrational frequencies, reactivity or other spectroscopic quantities, and cross sections for collision with other particles.

Computational chemistry methods range from highly accurate to very approximate; highly accurate methods such as the Ab initio electronic structure methods are based entirely on theory from first principles. The less accurate methods are normally called empirical or semi-empirical which employ experimental results, often from acceptable models of atoms or related molecules, to approximate some elements of the underlying theory.

Methods in Category

  • Ab inito methods
  • Density Functional methods
  • Semi-empirical and empirical methods
  • Molecular mechanics
  • Molecular dynamics

Software Packages

ab initio and DFT software packages

ab initio and DFT software packages available in SHARCNET software stack

Package License Basis sets Periodic Mol. Mech. HF Post-HF DFT
Gaussian commercial GTO any Y Y Y Y
NWChem academic GTO, PW any Y Y Y Y
ADF/BAND commercial GTO any Y Y N Y
Abinit GPL PW 3d Y N N Y
Quantum Espresso/PWSCF GPL PW 3d N Y N Y
SIESTA academic NAO Y N N Y

ab initio and DFT software packages run at SHARCNET by individual user(s)

Package License Basis sets Periodic Mol. Mech. HF Post-HF DFT
Molpro commercial GTO N N Y Y Y
Gamess (US) academic GTO N Y Y Y Y
Firefly/PCGamess academic GTO N Y Y Y Y
ASE/Dacapo GPL PW 3d Y N N Y
Wien2k commercial PW 3d Y N N Y
VASP commercial PW any Y N N Y

Molecular Dynamics software packages

Molecular Dynamics software packages available in SHARCNET software stack

Package License Description
AMBER commercial a set of molecular mechanical force fields for the simulation of biomolecules
Gromacs GPL designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers.
NAMD, VMD GPL a scalable molecular dynamics package written at the University of Illinois at Urbana Champaign which is particularly suited to biological applications. It uses Protein Data Bank files as the standard files for describing the configuration of atoms involved in the simulation, but it also provides compatibility with Amber parm and coordinate files, as well as Gromacs files. Unless specified otherwise, NAMD uses the CHARMM force field, but it is also able to implement the Amber force field.
CPMD GPL a parallelized plane wave/pseudopotential implementation of Density Functional Theory, particularly designed for ab-initio molecular dynamics.
LAMMPS GPL a classical molecular dynamics code for Large-scale Atomic/Molecular Massively Parallel Simulator.

Molecular Dynamics software packages run at SHARCNET by individual user(s)

Package License Description
CHARMM commercial Commercial version with multiple graphical front ends is sold by Accelrys (as CHARMm)
MOE commercial Molecular Operating Environment
Cosmos GPL Hybrid QM/MM COSMOS-NMR force field with fast semi-empirical calculation of electrostatic and/or NMR properties. 3-D graphical molecule builder and viewer.


Staff Contacts

The following staff have backgrounds in chemistry and biosystems and may be able to help with domain specific issues. Their contact information can be found in the SHARCNET staff directory.

  • Jemmy Hu
  • Pawel Pomorski