Update: stream link, further information and schedule are here: goo.gl/IjRCW9
This workshop brings together most of the core development team of GROMACS. Latest and upcoming developments of the code will be discussed. The program includes:
Electrostatic potential calculation
Fast Multipole methods
(Andreas Beckmann, Ivo Kabadshow, Thomas Ullmann)
Regular FMM, Berk Hess
Fast multipole methods, FMM combined with lambda-dynamics, PME improvements..
Free energy calculations and electrostatics
Using gromacs with experimental data
What applications are already implemented, what file formats are important to support.
Is there a common way gromacs is used/could be used for e.g. refinement against experimental data?
SAXS – refinement
(David van der Spool, Jochen Hub, Magnus Andersson)
Free Energy calculations
SoftCore Potential for numerically stable alchemical transformation and free energies based on Crooks Free Energy perturbation. (Vytautas Gapšys)
Constant pH simulation, dynamic-protonation simulation protocols
Gerrit Groenhof, Serena Donnini
the good, but not implemented yet, the bad and obsolete, and the ugly but useful
Gromacs user interface / accessibility
Get user feedback on what is clear, what tools are painful to use, what creates bottlenecks in the application.
Advanced User Lesson
Compute power optimisation through cluster and simulation set-up
How many nodes for my system size, balancing electrostatics calculations and particle-particle calculations. Tips and tricks to make your simulation faster. What is the optimal hardware to run gromacs on?
How To Do Development
Design of the gromacs codebase
Where to find what. I want to understand how , e.g. an analysis tool is implemented – where do I find that.. Current and target modularization state.
Compile your own gromacs
I made some changes to the gromacs source and want to run it on a cluster now – how do I achieve that.
Code review in gromacs
I’m confident that I made a useful contribution to gromacs – how does it become a part of the distribution?
Unit and regression test framework
How much do I need to cover with tests. What is already available in frameworks?
The C to C++11 transition
Best practices, most common coding mistakes. This is how we would like you to think about code.
Free energy calculations
pmx – (Vytautas Gapšys)
(Martin Mechelke, Benjamin von Ardenne, Dari Kimanius, Björn Forsberg)
cryo-EM refinement on GPU clusters
19 May, 2016 - 20 May, 2016