GROMACS 2016 Developer Workshop

GROMACS on highly parallel and heterogeneous platforms

On May 19–20, a group of >50 GROMACS developers and users gathered at the Max Planck Institute for biophysical Chemistry (today Max Planck Institute for Multidisciplinary Sciences) in Göttingen to discuss various aspects of software development and future directions for GROMACS.

GROMACS is an open-source software package for molecular simulations, with special focus on offering high performance on a wide-variety of HPC platforms. The growing variety and heterogeneity of the hardware platforms that need to be supported requires changes in code design. Therefore, recent improvements of the C++ language and how to exploit them for code portability and maintainability are discussed in this workshop. Moreover, advanced user lessons assist with hardware purchases that optimally fit the intended application and the available budget and simulation setup for maximum performance on a given HPC system. Besides hardware variety, also the number of practically relevant molecular mechanics force fields and simulation methods is growing. Recently, GROMACS has been extended to allow incorporation of experimental data from spectroscopy, crystallography and cryo-electron microscopy. An important workshop aim is also an agreement on standardized file formats and data annotation (e.g., experimental conditions, units of measured quantities) for reproducible and transferable use of experimental data. GROMACS has grown to a large-scale collaborative open source software project, which adds challenges in human resource management to the technological challenges. Questions of code maintainability, long-term support of features, code review, coding style are openly discussed.

The agenda contained talks and discussions about

  • the history and design principles of GROMACS,
  • how to do code development,
  • constant pH and lambda dynamics,
  • scalable electrostatics methods,
  • QM/MM,
  • external potentials,

and many more. Most of the talks were recorded (some weren't due to technical issues—sorry for that!) and can be found below. Due to legal regulations we can only make the talks public where we have an explicit agreement of the speakers, which also means that the discussion is not part of the following videos.

Slides of the talks (PDF files)

Erik Lindahl: Workshop Introduction

GROMACS history, design principles, new and coming in GROMACS 2016

Christian Blau: Scientific Code Development

How to do code development for GROMACS, best practices.

Berk Hess: Developing and contributing to GROMACS

How to get your code into GROMACS, or how to become a GROMACS developer.

Mark Abraham: GROMACS development, practices & problems

Gerrit Groenhof: Molecular dynamics at constant pH

Thomas Ullmann: A lambda-dynamics module for GROMACS

Ivo Kabadschow: Towards GROMACS with lambda-dynamics. FMM-based electrostatics.

Bartosz Kohnke: FMM - GPU implementation and lambda-dynamics

Berk Hess: FMM regularization

Carsten Kutzner: Compute power optimization by cluster & simulation setup

David van der Spoel, Jochen Hub: Structural changes of proteins in solution using SAXS/WAXS data

Christian Blau: External potentials from experimental data

Gerrit Groenhof: The road ahead for QM/MM in GROMACS

Thomas Kubar: QM/MM with DFTB3 in GROMACS

Katra Kolsek, Vedran Miletic: Reactive MD

Berk Hess: Accelerated Weight Histogram Method

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