GROMACS 2018-beta1 Release Notes

These release notes document the functionality changes that have taken place in GROMACS since version 2016.

Some bug fixes are mentioned here, but those fixed in 5.1 or 2016 branches are (or will be) documented there. If the same functionality is supported in both branches, bugs fixed on older branches can generally be assumed to be fixed in patch releases of subsequent major/minor versions.

Highlights

Here’s some highlights of what you can expect, along with more detail in the links below!

As always, we’ve got several useful performance improvements, with or without GPUs, and all enabled and automated by default. We are extremely interested in your feedback on how well this worked on your simulations and hardware. They are:

  • A new dual-list dynamic-pruning algorithm for the short-ranged interactions, that uses an inner and outer list to permit a longer-lived outer list, while doing less work overall.
  • PME long-ranged interactions can now run on a single GPU, which means many fewer CPU cores are needed for good performance.

There are some new features available also:

  • The AWH (Accelerated Weight Histogram) method is now supported, which is an adaptive biasing method used for overcoming free energy barriers and calculating free energies (see http://dx.doi.org/10.1063/1.4890371).
  • A physical validation suite is added, which runs a series of short simulations, to verify the expected statistical properties, e.g. of energy distributions between the simulations, as a sensitive test that the code correctly samples the expected ensemble.
  • Conserved quantities are computed and reported for more integration schemes - now including all Berendsen and Parrinello-Rahman schemes.

Details