finish up Gromacs engine readme

parent 45ada1c7
.. _ost_example:
.. _ops_gromacs_engine:
#################
OPS-based modules
#################
##################################
Gromacs engine in OpenPathSampling
##################################
.. sidebar:: Software Technical Information
......@@ -38,7 +38,33 @@ _________________
.. Give a brief overview of why the module is/was being created.
Different molecular dynamics (MD) codes have developed to serve different
communities. For example, although
communities. Gromacs is one of the major MD codes for the biomolecular
community, and even though much of its functionality can be reproduced by
other MD codes, such as OpenMM, there are still some extensions that are
built on top of Gromacs that haven't been ported to other codes. For
example, the MARTINI coarse-grained model is not available other codes such
as OpenMM.
Additionally, people who are familiar with a given MD package will prefer to
continue to work with that. Therefore codes that wrap around MD packages, as
OpenPathSampling does, can expand their reach by adding ways to interface
with other MD packages.
This module adds the Gromacs engine for OpenPathSampling. It is the first
practical test of the external engine API of OPS.
Specific functionality in this module includes:
* ``GromacsEngine``: the OPS dynamics engine, based on the
``ExternalEngine``, that runs Gromacs as an external tool. Option on
initialization allow the user to customize the path to the Gromacs
executable.
* ``ExternalMDSnapshot``: an OPS snapshot for external MD engines, which
contains coordinates, velocities, and box vectors. Requires that the
engine implement a ``read_frame_data`` method to load from a specific MD
trajectory.
* ``snapshot_from_gro``: a function that creates an OPS snapshot from a
Gromacs ``.gro`` file.
Background Information
......@@ -69,11 +95,11 @@ conda installed, this branch of OPS can be installed by downloading the
source conda_ops_dev_install.sh dwhswenson gromacs_engine
This will download a new copy of the git repository, select the
This will download a new copy of the OPS git repository, select the
``gromacs_engine`` branch from the ``dwhswenson`` fork, install the
requirements, and create an editable install of OPS. If you would like to do
this in a new conda environment, set the environment variable ``OPS_ENV``,
and it will install in a new environment with that the name ``$OPS_ENV``.
and it will install in a new environment with the name ``$OPS_ENV``.
To run tests, you may need ``pytest``, which can be installed with ``conda
install pytest``.
......
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