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GROMACS is a versatile package to perform molecular dynamics for systems with hundreds to millions of particles.

Description

GROMACS is a versatile package to perform molecular dynamics 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 and fluid dynamics.

Read more on the GROMACS home page.

For a manual consult the the GROMACS home page.

Strengths

  • GROMACS provides extremely high performance compared to all other programs.
  • GROMACS can make simultaneous use of both CPU and GPU available in a system. There are options to statically and dynamically balance the load between the different resources.
  • GROMACS is user-friendly, with topologies and parameter files written in clear text format.
  • Both run input files and trajectories are independent of hardware endian-ness, and can thus be read by any version GROMACS.
  • GROMACS comes with a large selection of flexible tools for trajectory analysis.
  • GROMACS can be run in parallel, using the standard MPI communication protocol.
  • GROMACS contains several state-of-the-art algorithms.
  • GROMACS is Free Software, available under the GNU Lesser General Public License (LGPL).

Weaknesses

  • GROMACS does not do to much further analysis to get very high simulation speed.
  • Sometimes it is challenging to get non-standard information about the simulated system.
  • Different versions sometimes have differences in default parameters/methods. Reproducing older version simulations with a newer version can be difficult.
  • Additional tools and utilities provided by GROMACS are sometimes not the top quality.

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GROMACS Tools

VMD

Useful links

References

  1. GROMACS User-Guide
  2. PLUMED Home