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OpenScience / Software / Chemistry / Theoretical and Computational
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
Posted in Molecular Dynamics
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OpenMM
OpenMM is a toolkit for molecular simulation. It can be used either as a stand-alone application for running simulations, or as a library you call from your own code. It provides a combination of extreme flexibility (through custom forces and … Continue reading
Posted in Theoretical and Computational
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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
Posted in Molecular Dynamics
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NWChem
NWChem aims to provide its users with computational chemistry tools that are scalable both in their ability to treat large scientific computational chemistry problems efficiently, and in their use of available parallel computing resources from high-performance parallel supercomputers to conventional … Continue reading
Posted in Ab Initio Quantum Chemistry
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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/
Posted in Molecular Dynamics
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MESMER
MESMER (Master Equation Solver for Multi Energy-well Reactions) models the interaction between collisional energy transfer and chemical reaction for dissociation, isomerisation, association, and non-adiabatic hopping processes. Find MESMER at: http://www.chem.leeds.ac.uk/mesmer.html
Posted in Theoretical and Computational
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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
Posted in Molecular Dynamics
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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
Quantum-Espresso
Quantum ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials (both norm-conserving and ultrasoft). Find Quantum-Espresso at: http://www.quantum-espresso.org
Posted in Ab Initio Quantum Chemistry
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The CP2K project homepage
CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different methods such as e.g. density functional theory (DFT) … Continue reading
Posted in Theoretical and Computational
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