Using the Python package

After installing GROMACS, sourcing the “GMXRC” (see GROMACS docs), and installing the gmxapi Python package (see Full installation instructions), import the package in a Python script or interactive interpreter. This documentation assumes a convenient alias of gmx to refer to the gmxapi Python package.

import gmxapi as gmx

For full documentation of the Python-level interface and API, use the pydoc command line tool or the help() interactive Python function, or refer to the procedural interface documentation.

Python does not wrap any command-line tool, so once installation is complete, there shouldn’t be any additional configuration necessary, and any errors that occur should be caught at the Python level. Any Python exception raised by gmxapi should be descended from (and catchable as) gmxapi.exceptions.Error.

As an exception to the preceding paragraph, we have a tool specifically for wrapping arbitrary (unintegrated) command line tools: See gmxapi.commandline_operation.

Running simulations


The work graph


Synchronous and asynchronous work

Accelerated computation

Simulation input

Preparing simulation input

With work graph operations

With file utilities

Manipulating simulation parameters

With key word arguments

With work graph operations

Accessing trajectory data

From files

From in-memory objects

From gmxapi operation results