Category Archives: Theoretical and Computational

AMBER

AMBER is group of programs used for simulation of biomolecules. It is highly efficient parallel MD simulation program written in FORTRAN. Find AMBER at: http://ambermd.org/

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XMD

XMD is a GPL’ed Molecular Dynamics program written in C. It supports the following potentials: pair, EAM, Tersoff and Stillinger-Weber, and implements a large variety of commands to help simplify simulation. Find XMD at: http://xmd.sf.net

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Zori

Zori is an open-source quantum monte carlo package for the electronic structure of atoms and molecules. Find Zori at: http://www.zori-code.com

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Protomol

ProtoMol is a high-performance framework in c++ for rapid prototyping of novel algorithms for molecular dynamics and related applications. Its flexibility is achieved primarily through the use of inheritance and design patterns (object-oriented programming). Performance is obtained by using templates … Continue reading

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LAMMPS

LAMMPS is a classical molecular dynamics code that models an ensemble of particles in a liquid, solid, or gaseous state. It can model atomic, polymeric, biological, metallic, or granular systems using a variety of force fields and boundary conditions. Find … Continue reading

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MCCCS Towhee

Towhee is a Monte Carlo molecular simulation code originally designed for the prediction of fluid phase equilibria using atom-based force fields and the Gibbs ensemble with particular attention paid to algorithms addressing molecule conformation sampling. The code has subsequently been … Continue reading

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OOPSE

OOPSE is a new molecular dynamics simulation program which is capable of efficiently integrating equations of motion for atom types with orientational degrees of freedom (e.g. "sticky" atoms and point dipoles). Transition metals can also be simulated using the embedded … Continue reading

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The Molecular Workbench Software

The Molecular Workbench is a set of tools that can be used to compute and visualize the motion of ensembles of atoms and molecules. The motion of each entity is estimated using classical dynamics and applicable forces, including van der … Continue reading

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PSI3

The PSI3 suite of quantum chemical programs is designed for efficient, high-accuracy calculations of properties of small to medium-sized molecules. The package’s current capabilities include a variety of Hartree-Fock, coupled cluster, complete-active-space self-consistent-field, and multi-reference configuration interaction models. Find PSI3 … Continue reading

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GROMACS

GROMACS is a very fast molecular dynamics code, which comes with lots of features like PME, a variety of cut-offs, non-equilibrium MD and more. The package includes also other algorithms like normal mode analysis and essential dynamics plus a wealth … Continue reading

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