BioSimSpace

A new software framework to create an interoperability layer around the many software packages that are already embedded within the biosimulation community. BioSimSpace will enable rapid development of workflows between these software packages that can then be used in conjunction with existing workflow software such as Knime, Pipeline Pilot, ExTASY etc. This project is currently in an early phase of development, more information can be found here.

FESetup

 

FESetup 1.2.1
(1 vote)

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.

Support: A mailing list for user support can be subscribed to here.

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Other Software:

FFEA - Fluctuating Finite Element Analysis.

Longbow - a HECBioSim tool for HPC job submission.

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.