Category Archives: Molecular Dynamics

compute_fep

Free energy perturbation for LAMMPS, with soft-core pair potentials. Uses FEP, Thermodynamic Integration (TI), Mezei FDTI, and Bennet Acceptance Ratio methods. It can be used for alchemical transformations of pair potentials or charges in selected atoms. Find compute_fep at: https://github.com/agiliopadua/compute_fep

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Molecular Dynamics Studio

This is a collection of software modifications created to integrate NanoEngineer-1, PACKMOL and MSI2LMP for the purpose of easily creating molecular dynamics cells. NanoEngineer-1 is a molecular CAD software written by Nanorex and provides the user an easy way to … Continue reading

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fOOm-d

fOOm-d (framework for Object Oriented molecular dynamics) is a molecular dynamics framework with an emphasis on methods that require coupling of separate trajectories – e.g., EVB methods and a range of classical-trajectory guided quantum dynamics methods Find fOOm-d at: http://foom-d.sourceforge.net/

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OpenMD

OpenMD is an open source molecular dynamics engine which is capable of efficiently simulating liquids, proteins, nanoparticles, interfaces, and other complex systems using atom types with orientational degrees of freedom (e.g. sticky atoms, point dipoles, and coarse-grained assemblies). Proteins, zeolites, … Continue reading

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Ascalaph

Package of molecular graphics and dynamics with an interface to quantum chemistry. GPL Find Ascalaph at: http://www.biomolecular-modeling.com/Ascalaph/index.html

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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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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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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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