Newly released GROMACS 2019.4 Patch is available for download now. These release notes document the changes that have taken place in GROMACS since the previous 2019.3 version, to fix known issues. It also incorporates all fixed made in version 2018.7 and earlier, which you can find described in the Release notes.

What is GROMACS?

GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.

It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers.

Cryo-em GPUs

Major Fixes and Changes:

  • Fixes where mdrun could behave incorrectly
    • Fix incorrect LJ cut-off on GPU when rvdw < rcoulomb
    • Fix (unlikely) missing bonded forces with CUDA GPUs and domain decomposition
    • Fix incorrect reporting of final kinetic energy and temperature
    • Fix segmentation fault in grompp and mdrun with cosine COM pulling
  • Fixes for gmx tools
    • Fix grompp not adding angle constraints between constraints
    • Fix gmx wham with angle and dihedral geometries
    • Fix bug in gmx xpm2ps
    • Fix bug in gmx anaeig
    • Fix issue with demux.pl script
    • Made gmx disre work with non-consecutively labeled restraints
    • Fixed writing of gro files with index groups
    • Made gmx make_ndx keep chain IDs
  • Fixes that affect portability
    • Disable PME OpenCL on Apple
  • Added AMD Zen 2 detection

Preview of the GROMACS Documentation Release 2019.4

Here is a quick preview of some of the items you will be learning about in the documentation release.

  • Introduction to building GROMACS
    • Quick and dirty installation
    • Quick and dirty cluster installation
    • Typical installation
    • Building older versions
  • Getting Started
    • Flow Chart
    • Setting up your environment
    • Flowchart of typical simulation
    • Important files
    • Tutorial material
    • Background reading
  • System Preparation
    • Steps to consider
    • Tips and tricks
  • Managing long simulations
    • Appending to output files
    • Backing up your files
    • Extending a .tpr file
    • Changing mdp options for a restart
    • Restarts without checkpoint files
    • Are continuations exact?
    • Reproducibility

Download the complete full documentation to learn more – http://manual.gromacs.org/2019.4/download.html

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