Notes on the Python level of the package.

Other Python Gromacs interfaces

  • gmxscript : all-python CLI
    wrapper manages files, provides “checkpointed” re-runnable workflow with mdp rewriting and CLI replacement
  • GromacsWrapper
    (Beckstein) : all-python CLI wrapper provides thorough scriptable interface with error handling
  • pmx (D. Seeliger) : Manipulate
    Gromacs files and data structures
  • grompy (Rene Pool) : patches old Gromacs
    code to provide ctypes interface to Gromacs libraries
  • gmx_wrapper : very
    bare-bones CLI wrapper
  • GromacsPipeline
    (Redmine 1625) adds SIP bindings to run Gromacs analysis modules in a single pass on a trajectory

Existing Python tools to leverage

Some of the tools available from the gmx command-line interface are bundled largely for convenience, and Python users may be better served by turning to other projects rather than relying on exposing redundant functionality from libgromacs. In other cases, Gromacs developers may simply want to be aware of the other tools and interoperability requirements.

  • pypdb A Python API for the RCSB Protein Data Bank (PDB)
  • chemlab Qt-powered molecular viewer
  • chemview molecular viewer for IPython from the author of chemlab
  • MDTraj Read, write and analyze MD trajectories
  • MDAnalysis analyze trajectories from molecular dynamics
  • Biopython tools for computational molecular biology
  • several packages named “Biopy” do not seem relevant
  • PyMOL molecular viewer
  • mmLib Python Macromolecular Library analysis, manipulation, and viewing
  • msmbuilder Statistical models for Biomolecular Dynamics
  • PyEMMA estimation, validation and analysis Markov models from molecular dynamics (MD) data
  • ExSTACY Collection of tools that couples large ensemble Molecular Dynamics calculations with analysis to provide improvements in sampling. Includes
  • EnsembleMD framework for running ensemble workflows
  • COCO
  • LSDMap Locally Scaled Diffusion Maps
  • pyPcazip principle component analysis
  • Plumed free energy calculation using collective variables
  • pdb tools
  • OpenMM
  • msmbuilder
  • BioXL


The package should have a name that does not collide with other known projects, particularly any projects on pypi. “gmx” is available on pypi, but similar existing package names include

  • gmx-script
  • python-gmx

pygmx is the name used for a bindings package posted to the Gromacs list that resides at

There are several packages named grompy

The Beckstein lab has GromacsWrapper which exists on, GitHub, and PyPi.

Note that our CMake project is called gmxpy through (at least) release 0.0.7.

Python version

The Python 2 end-of-support has been extended to 2020. It is reasonable to assume that Python 2.7.15 is the final version of Python 2 and that it will be officially end-of-lifed in 2020. On the one hand, Python 2 will be a mature language with no further interface changes. On the other hand, the loss of the commitment to bug fixes means it has already started fading away.

Python 3.3 has a lot of improvements and changes, including better 2.7 compatibility

Python 3.4

  • built-in pip
  • enum types
  • new pickle protocol

Python 3.5

  • typing and coroutines
  • RecursionError exception
  • Generators have gi_yieldfrom
  • memoryview tuple indexing
  • hexadecimal methods

Linux distributions released after June 2013 and supported at least to June 2019.

Ubuntu 14.04 (trusty): Python 3.4
Ubuntu 16.04 (denial): Python 3.5
Debian 8 (jessie): Python 3.4
Debian 9 (stretch): Python 3.5
Linux Mint 18 (rosa): 3.4
Linux Mint 17 (sarah): 3.5
Fedora 23: 3.4
Fedora 24+: 3.5
RHEL 7: n/a
CentOS 7: n/a

gmxapi policy

GROMACS will officially switch from Python 2.7 to Python 3+ during the GROMACS 2020 development cycle for its infrastructure. gmxapi 0.0.7 officially supports Python 2.7 and Python 3.4+. gmxapi will continue to support Python 2.7 for as long as is feasible, but should default to Python 3 style and syntax. As much as possible, current code is in a version-agnostic style, avoiding dependencies on 3to2 or six. Future versions may use compatibility tools. At some point, Python 2 compatibility will be achieved with conversion tools during package installation instead of in the Python source code so that we can remove from __future__ imports and other clunky work-arounds.