Computational Chemistry/Molecular Modeling

AMBER
AMBER (Assisted Model Building with Energy Refinement) is a package of molecular simulation programs. Version 9 is currently installed on Biowulf. Major programs in the AMBER package include sander, gibbs, nmode, LEap.

APBS
APBS (Adaptive Poisson-Boltzmann Solver) is a software package for the numerical solution of the Poisson-Boltzmann equation (PBE), one of the most popular continuum models for describing electrostatic interactions between molecular solutes in salty, aqueous media.

Autodock
is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure.

CHARMM on Biowulf
CHARMM (Chemistry at HARvard Molecular Mechanics) is a program which supports a wide range of theoretical modeling calculations of the structure and dynamics of biological molecules. In addition to energy minimization and molecular dynamics simulations, Monte Carlo sampling, use of genetic algorithms, and several interfaces to quantum codes (AM1, GAMESS) are available or under development. Recent CHARMM versions have been made available for use on Biowulf, as a joint effort between NHLBI/LBC Computational Biophysics Section and CBER/OVRR Biophysics Lab and with the support of Biowulf Staff. Multiple executables are available for each version, in order to support larger molecular systems, and the different types of parallel communications available on Biowulf, i.e. ethernet and Myrinet 2000. The support files are also available for the above versions, e.g. version .doc files, and the standard topology and parameter files.

CHARMM is a fairly sophisticated and complicated command line based program; detailed CHARMM Documentation is available online.

GAMESS
GAMESS is a program for ab initio quantum chemistry. Briefly, GAMESS can compute wavefunctions ranging from RHF, ROHF, UHF, GVB, and MCSCF, with CI and MP2 energy corrections available for some of these. Analytic gradients are available for these SCF functions, for automatic geometry optimization, transition state searches, or reaction path following. Computation of the energy hessian permits prediction of vibrational frequencies. A variety of molecular properties, ranging from simple dipole moments to frequency dependent hyperpolarizabilities may be computed. Many basis sets are stored internally, and together with effective core potentials, all elements up to Radon may be included in molecules. Several graphics programs are available for viewing of the final results. Many of the computational functions can be performed using direct techniques, or in parallel on appropriate hardware.

GAUSSIAN 03
Gaussian 03 is a series of electronic structure programs performing computations starting from the basic laws of quantum mechanics. Gaussian can predict energies, molecular structures, vibrational frequencies for systems in the gas phase and in solution, and it can model them in both their ground state and excited states.

GROMACS
is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. It is primarily designed for biochemical molecules like proteins and lipids 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
NAMD is a parallel molecular dynamics program for UNIX platforms designed for high-performance simulations in structural biology. It is developed by the Theoretical Biophysics Group at the Beckman Center, University of Illinois. NAMD is particularly well suited to Beowulf clusters, as it was specifically designed to run efficiently on parallel machines.
VMD, the molecular visualization program integrated with NAMD, is also available on the Helix Systems.

PROSPECT
PROSPECT is a threading-based protein structure prediction system. PROSPECT will find structural homologs of a target sequence, even when the structural homolog sequences have insignificant identity to the target sequence.

Q-Chem
is an ab initio electronic structure program capable of performing first principles calculations on both the ground and excited states of molecules.

Schrödinger
A limited number of Schrödinger applications (such as MacroModel, Jaguar, and QikProp) are available through the Molecular Modeling Interest Group.