This page lists all of the software tools developed by the ExTASY project with brief descriptions along with links to where you can obtain the code and find further documentation. Most of the tools can also be found via our Bitbucket pages
The Ensemble MD Toolkit is a Python library for developing and executing large-scale ensemble-based Molecular Dynamics (MD) simulations and workflows, based on RADICAL-Pilot
A tool to run multiple Molecular Dynamics simulations which can be coupled to an Analysis stage. This forms a simulation-analysis loop which can be made to iterate multiple times. Two example workflows are provided: COCO with AMBER and LSDMap with Gromacs (DM-d-MD)
ExTASY wrappers provide a consistent API for launching command line applications (such as MD simulations or simulation analysis jobs) from python scripts. Though designed originally with ExTASY simulation-analysis workflows in mind, they are extensible to many other possible applications.
LSDMap is a program to compute Locally Scaled Diffusion Maps. The eigenvectors of the diffusion matrix can be used to form a small set of reaction coordinates describing the behaviour of a high-dimensional data set such as an equilibrium MD trajectory.
CoCo, which is based on principal component analysis, analyses the distribution of an ensemble of structures in conformational space, and generates a new ensemble that fills gaps in the distribution. The package provides a python-based command line tool that implements the CoCo method, and also exemplifies its application within an ExTASY workflow that can be used in an iterative manner to rapidly expand the coverage of a MD-generated ensemble.
pyPcazip is a Python-based suite of software tools for Principal Component Analysis of molecular dynamics simulation data, and also for its compression. It is compatible with trajectory file formats generated by most contemporary MD engines such as AMBER, CHARMM, GROMACS and NAMD, and is MPI parallelized to permit the efficient processing of very large datasets.
MIST (Molecular Integration Simulation Toolkit) is a C++ library which provides two things - a simple API for integrator developers which hides the complexities of real MD codes, enabling rapid development of new integration algorithms at a higher level of abstraction; and a plug-in interface, enabling the new integrators to be deployed directly in several MD codes, taking advantage of their highly efficient force evaluation code, file format support, and supporting tool chains.