Molecular Integration Simulation Toolkit - interfacing novel integrators with Molecular Dynamics codes

Research output: Contribution to conferenceAbstractpeer-review

Abstract

Modern production Molecular Dynamics codes represent a significant investment of effort by the community to develop highly optimised force evaluation routines able to take advantage of state-of-the art hardware such as GPUs and multi-core CPUs. However, this comes at a cost of code complexity which makes it hard for new integration algorithms to be implemented in these packages. This creates a catch-22 for algorithm developement - if new algorithms cannot be implemented and tested in production codes it may be impossible to demonstrate their benefits over existing schemes; conversely, if the community cannot see the benefit of new algorithms, code developers will not spent time implementing them!
The Molecular Integration Simulation Toolkit (MIST) library is a solution to this problem by providing plug-ins to existing optimised MD codes, coupled with a simple interface for the development of new integration methods. MIST currently provides interfaces to GROMACS, Amber and NAMD-Lite, allowing it to benefit from OpenMP and GPU acceleration for force-evaluation. Several standard (Verlet, Leapfrog) and new (Langevin Dynamics based on a BAOAB splitting) integrators have been implemented to date. The MIST library interface results in significant ease-of-development, at negligible loss of performance. New integration algorithms are implemented once, in a code-agnostic manner, and can then be immediately deployed in all the MD codes supported by MIST.
As well as algorithms for sampling the canonical and micro-canonical ensembles, MIST is also a platform for building more advanced schemes. For example, we have implemented an extended-system method for 'Continuous Tempering', which enables computation of free energy maps in systems with large energy barriers.
Several new features are under development in MIST - new constraint solvers for extremely long timesteps and multi-timestep splittings, MPI parallelisation, and support for more MD codes. We welcome the community's input on direction for future development.
Original languageEnglish
Publication statusPublished - 19 Jun 2016
EventISQBP President's Meeting 2016 - Bergen, Norway
Duration: 19 Jun 201622 Jun 2016

Conference

ConferenceISQBP President's Meeting 2016
CountryNorway
CityBergen
Period19/06/1622/06/16

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  • ISQBP President's Meeting 2016

    Iain Bethune (Speaker)

    19 Jun 201622 Jun 2016

    Activity: Participating in or organising an event typesParticipation in conference

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