Name: conda-gromacs-2016
Owner: Becksteinlab
Description: Conda package of gromacs 2016 intended for testing purposes.
Created: 2016-09-21 23:48:53.0
Updated: 2017-02-28 00:22:32.0
Pushed: 2017-02-28 00:18:33.0
Size: 6
Language: Shell
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This repository contains everything needed to build conda packages for the popular Gromacs molecular dynamics package.
WARNING: The package builds a minimal, portable Gromacs version that is primarily useful for testing. It is not recommended to use it for production-scale simulations.
Reduced performance features:
Multiple versions of Gromacs can be installed in parallel. A script
get_gmx
is installed in the user's home directory that allows the
user to select the desired version of Gromacs. It returns the path to
the GMXRC
startup script, which in turn needs to be sourced to set
up the Gromacs environment. For instance, to select version
2016 one would run in the shell
ce `get_gmx 2016`
Anaconda packages for linux-64 are available in the Anaconda Cloud channel
anaconda.org/becksteinlab. If you
have conda
installed you can install this package with
a install -c becksteinlab gromacs-2016
It is recommended to build the package within a minimal docker container. Build the docker container by invoking
er build -t gmx_build .
in the same directory as the provided Dockerfile.
Start the docker container with docker run -it gmx_build
. If everything
works as expected, then you should find yourself in an environment similar
to:
t@0f6a75177395 /]#
Navigate to /root/gromacs
to find the build scripts. Run:
build_conda_package.sh
Once this has finished move to the parent directory to find your package in tar.bz2 archive.
From a new terminal find the container ID with docker ps
. With this ID, invoke:
er cp <CONTAINER ID>:/root/<CONDA_TAR_BZ2> $OUTPUT_DIR
You should be able to find the conda package in the output directory.
To exit the docker container type exit
.
To upload directly to a the Anaconda clound through your Anaconda username, run:
onda upload -u <ANACONDA USERNAME> <CONDA_TAR_BZ2>
To exit the docker container type exit
Gromacs itself is published
under the GNU
Lesser General Public License
(LGPL), version 2.1. The files to build anaconda packages are
licensed under the MIT license (see file LICENSE
).
We welcome contributions in the form of issue reports and pull requests.