Workshop: GROMACS on highly parallel and heterogeneous platforms

Update: stream link, further information and schedule are here:

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:

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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 operare in borsa con le opzioni 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)

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SoftCore Potential for numerically stable alchemical transformation and free energies based on Crooks Free Energy perturbation. (Vytautas Gapšys)

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Gerrit Groenhof, Serena Donnini

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Gerrit Groenhof

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Get user feedback on what is clear, what tools are painful to use, what creates bottlenecks in the application.

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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?

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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.

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Free energy calculations

Lambda Dynamics

pmx – (Vytautas Gapšys)

reactive MD


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XFEL refinement

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

cryo-EM refinement on GPU clusters


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19 May, 2016 - 20 May, 2016
All Day

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Max Planck Institute for Biophysical Chemistry


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