Workshop: GROMACS on highly parallel and heterogeneous platforms



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:

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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

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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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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.

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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

(Vedran)

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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

Categories

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