Macs in Chemistry

Insanely Great Science

GROMACS updated

 

The official release of GROMACS 2018 is now available.

GROMACS is one of the major software packages for the simulation of biological macromolecules.

Highlights from this update include:-

  • PME long-ranged interactions can now run on a single GPU, which means many fewer CPU cores are needed for good performance.
  • Optimized SIMD support for recent CPU architectures: AMD Zen, Intel Skylake-X and Skylake Xeon-SP.

  • 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 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 and making runs less sensitive to the choice of the “nslist” parameter.
  • 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.

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