A new software framework to create an interoperability layer around the many software packages that are already embedded within the biosimulation community. BioSimSpace enables rapid development of workflows between these software packages that can then be used in conjunction with existing workflow software. More information can be found on the project website.
A tool to automate setup for alchemical relative free energy simulations with Molecular Dynamics and Monte Carlo, and a tool for general simulation setup like equilibration.
Citation: A detailed description has been published in DOI: 10.1021/acs.jcim.5b00368. Please cite this when you use FESetup.
Documentation: The FESetup documentation can be found here.
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FFEA - Fluctuating Finite Element Analysis.
ProtoMS - a complete protein Monte Carlo free energy simulation package.
Sire - a complete python/C++ molecular simulation framework, particularly focussed around Monte Carlo, QM/MM and free energy methods.
PCAZIP - a toolkit for compression and analysis of molecular dynamics trajectories.
COCO - a tool to enrich an ensemble of structures, obtained e.g. from NMR.
Handy Routines for Ptraj/Cpptraj - additional analysis methods for ptraj and cpptraj.