Simulation Codes

AMBER — by pul7 — last modified May 07, 2008 03:09 PM

AMBER (an acronym for Assisted Model Building and Energy Refinement) is a family of force fields for molecular dynamics of biomolecules. AMBER is also the name for the molecular dynamics simulation package.

Gaussian — by pul7 — last modified May 07, 2008 03:22 PM

Gaussian: Starting from the basic laws of quantum mechanics, Gaussian predicts the energies, molecular structures, and vibrational frequencies of molecular systems, along with numerous molecular properties derived from these basic computation types. It can be used to study molecules and reactions under a wide range of conditions, including both stable species and compounds which are difficult or impossible to observe experimentally such as short-lived intermediates and transition structures. This article introduces several of its new and enhanced features. For more information visit:

VASP — by pul7 — last modified May 07, 2008 03:39 PM

VASP: VAMP/VASP is a package for performing ab-initio quantum-mechanical molecular dynamics (MD) using pseudopotentials and a plane wave basis set. The approach implemented in VAMP/VASP is based on a finite-temperature local-density approximation (with the free energy as variational quantity) and an exact evaluation of the instantaneous electronic ground state at each MD-step using efficient matrix diagonalization schemes and an efficient Pulay mixing. These techniques avoid all problems occurring in the original Car-Parrinello method which is based on the simultaneous integration of electronic and ionic equations of motion. The interaction between ions and electrons is described using ultrasoft Vanderbilt pseudopotentials (US-PP) or the projector augmented wave method (PAW). Both techniques allow a considerable reduction of the necessary number of plane-waves per atom for transition metals and first row elements. Forces and stress can be easily calculated with VAMP/VASP and used to relax atoms into their instantaneous groundstate.