Jul 15, 2015
Macromolecular Simulation Software Workshop featuring OpenMM
By Joy Ku
Increase your expertise with OpenMM at CECAM’s Macromolecular Simulation Software Workshop. OpenMM developer Peter Eastman and OpenMM power user John Chodera will help run the sub-workshop on “Developing interoperable and portable molecular simulation software libraries,” which will teach attendees how to develop code with OpenMM and the free energy calculations library Plumed.
Macromolecular Simulation Software Workshop
Dates: October 12, 2015 to October 25, 2015
Location: CECAM-DE-JUELICH, Juelich, Germany
Application deadline: July 27, 2015. Each sub-workshop is limited to 30 participants
Registration and more information: http://www.cecam.org/workshop-1214.html
Biomolecular simulation continues to grow in popularity and scope of application. It is no longer the preserve of a few specialist groups but is widespread - part of the ‘toolkit’ used by researchers in a wide variety of fields, often closely integrated with other experimental research techniques. As the use of biomolecular simulation grows, a corresponding boom in (decentralised) software development is taking place.
This workshop is formatted as six sequential workshops, each 2 days long, that enable participants to learn about many different aspects of biomolecular simulation software:
• Software development and engineering
• Simulation data analysis
• Setting up simulations
• Development of software libraries
• High-performance distributed computing tools
• Advanced sampling and long timescale molecular dynamics.
Participants will be able to attend all sub-workshops or just a subset of them. In the process, they will learn about many biomolecular simulation software that are available, including:
• OpenMM (https://openmm.org) - part of the Omnia suite of biomolecular simulation tools (http://omnia.md),
• MMTK (http://dirac.cnrs-orleans.fr/MMTK/),
• MDAnalysis (https://code.google.com/p/mdanalysis/) ,
• MDTraj (http://mdtraj.org),
• SIRE (http://siremol.org/Sire/Home.html),
• Bookshelf (http://sbcb.bioch.ox.ac.uk/bookshelf/)
as well as more general-purpose Python-based tools that have clear applicability to biosimulation – e.g. RADICAL-Cybertools (http://radical-cybertools.github.com).
To register or learn more about the workshop, visit http://www.cecam.org/workshop-1214.html.
There is no registration fee for the workshop, but accommodation, meals and all other travel costs must be covered by participants. Some funding may be provided by NSF to enable US early career researchers to attend the workshop.