SI2-CHE: ExTASY: Extensible Tools for Advanced Sampling and analYsis
Lead Research Organisation:
University of Edinburgh
Department Name: Sch of Mathematics
Abstract
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Publications
Balasubramanian V
(2016)
ExTASY: Scalable and flexible coupling of MD simulations and advanced sampling techniques
Banisch R
(2017)
Understanding the geometry of transport: Diffusion maps for Lagrangian trajectory data unravel coherent sets.
in Chaos (Woodbury, N.Y.)
Bethune I
(2019)
MIST: A simple and efficient molecular dynamics abstraction library for integrator development
in Computer Physics Communications
Boninsegna L
(2015)
Investigating Molecular Kinetics by Variationally Optimized Diffusion Maps.
in Journal of chemical theory and computation
Di Pierro M
(2015)
A Stochastic Algorithm for the Isobaric-Isothermal Ensemble with Ewald Summations for All Long Range Forces.
in Journal of chemical theory and computation
Frank J
(2015)
Direct control of the small-scale energy balance in two-dimensional fluid dynamics
in Journal of Fluid Mechanics
Gobbo G
(2015)
Extended Hamiltonian approach to continuous tempering.
in Physical review. E, Statistical, nonlinear, and soft matter physics
Leimkuhler B
(2017)
Ensemble preconditioning for Markov chain Monte Carlo simulation
in Statistics and Computing
Leimkuhler B
(2015)
On the numerical treatment of dissipative particle dynamics and related systems
in Journal of Computational Physics
| Description | We developed new algorithms and preliminary software implementations for those algorithms. |
| Exploitation Route | We have created the MIST toolkit which allows modification of large scale molecular dynamics simulation codes. Examples of codes we currently support include NAMD Lite and Gromacs. We are currently working on additional plugins to support AMBER. We have begun preliminary studies for the treatment of constraints. |
| Sectors | Chemicals,Pharmaceuticals and Medical Biotechnology |
| URL | http://extasy-project.org |
| Description | ARCHER eCSE |
| Amount | £65,250 (GBP) |
| Funding ID | eCSE08-20 |
| Organisation | ARCHER |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 08/2016 |
| End | 11/2017 |
| Description | EPSRC Responsive Mode |
| Amount | £304,822 (GBP) |
| Funding ID | EP/P006175/1 |
| Organisation | Engineering and Physical Sciences Research Council (EPSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 01/2017 |
| End | 12/2019 |
| Title | g-BAOAB source files |
| Description | The files included here are the code files needed to implement the geodesic integration schemes relevant to the manuscript: "Efficient molecular dynamics using geodesic integration and solvent-solute splitting" (Proceedings of the Royal Society, 2016). |
| Type Of Material | Database/Collection of data |
| Year Produced | 2016 |
| Provided To Others? | Yes |
| Description | John Chodera/Memorial Sloan Kettering Cancer Centre |
| Organisation | Memorial Sloan Kettering Cancer Center |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | Collaborated on numerical method analysis and error quantification. We provided theoretical support in the discussions. |
| Collaborator Contribution | numerical implementations in software, testing |
| Impact | Multidiscipinary, combining mathematics, chemistry, physic and biological sciences Publication: Quantifying Configuration-Sampling Error in Langevin Simulations of Complex Molecular Systems, Josh Fass, David A. Sivak, Gavin E. Crooks, Kyle A. Beauchamp, Benedict Leimkuhler and John D. Chodera Entropy 2018, 20(5), 318. |
| Start Year | 2017 |
| Description | Materials Studio / MIST Integration |
| Organisation | Dassault Group |
| Department | BIOVIA |
| Country | United States |
| Sector | Private |
| PI Contribution | We have planned and implemented an interface between the MIST library and Forcite, a classical molecular dynamics code which is part of the Materials Studio package developed by Dassault Systemes BIOVIA. We have tested the Langevin dynamics integration scheme developed at UoE and discussed plans for further functionality, laying the groundwork for a longer-term engagement with BIOVIA. |
| Collaborator Contribution | BIOVIA staff have hosted two visits from UoE staff, and given us support and training on the design and implementation of Forcite, enabling us to complete the interface between MIST & Forcite very easily. |
| Impact | A prototype version of Forcite with MIST library support is under evaluation by BIOVIA for future inclusion in the Materials Studio product. |
| Start Year | 2017 |
| Title | ExTASY toolkit (pre-release) |
| Description | ExTASY is a flexible software toolkit which addresses one of the "Grand Challenges in the Chemical Sciences", namely the ability to understand the properties of complex macromolecular systems by effective sampling of their conformational space using Molecular Dynamics. The toolkit couples large ensemble MD calculations, with novel analysis methods and efficient integrators, to support orders-of-magnitude faster sampling. |
| Type Of Technology | Software |
| Year Produced | 2014 |
| Open Source License? | Yes |
| Impact | n/a |
| URL | http://extasy-project.org |
| Title | MPI-parallel version of PCAZIP |
| Description | Principal Component Analysis (PCA) forms the basis of a powerful range of simulation analysis methods, and also provides an approach to very efficient trajectory data compression. The pyPcazip package is a re-implementation by the ExTASY project www.extasy-project.org of the PCAZIP toolkit developed and distributed by the Laughton Group at the University of Nottingham, UK, and the Orozco group at the University of Barcelona, Spain. |
| Type Of Technology | Software |
| Year Produced | 2014 |
| Open Source License? | Yes |
| Impact | n/a |
| URL | https://bitbucket.org/ramonbsc/pypcazip/overview |
| Title | Molecular Integration Simulation Toolkit |
| Description | A library of integration routines for molecular dynamics that can be interfaced to a range of popular molecular dynamics codes for force evaluation (currently NAMD-Lite only). |
| Type Of Technology | Software |
| Year Produced | 2019 |
| Open Source License? | Yes |
| Impact | n/a |
| URL | https://bitbucket.org/extasy-project/mist |