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:

Gromacs Directions

Electrostatic potential calculation

Fast Multipole methods

(Andreas Beckmann, Ivo Kabadshow, Thomas Ullmann)

Regular FMM, Berk Hess

PME improvements

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

QM/MM simulations

Gerrit Groenhof

Analysis Tools

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.

Workflow Tools

Free energy calculations

Lambda Dynamics

pmx – (Vytautas Gapšys)

reactive MD



XFEL refinement

(Martin Mechelke, Benjamin von Ardenne, Dari Kimanius, Björn Forsberg)

cryo-EM refinement on GPU clusters