README for conda-gromacs-2016

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:

• only thread parallelization
• uses bundled FFT (not a fast FFT)
• no GPU support

Using the installed package

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

source `get_gmx 2016`

Pre-built packages

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

conda install -c becksteinlab gromacs-2016

Building the package

It is recommended to build the package within a minimal docker container. Build the docker container by invoking

docker 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:

[root@0f6a75177395 /]# 

Navigate to /root/gromacs to find the build scripts. Run:

bash build_conda_package.sh

Once this has finished move to the parent directory to find your package in tar.bz2 archive.

Keep locally or push to cloud:

Copy to host machine

From a new terminal find the container ID with docker ps. With this ID, invoke:

docker 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.

Upload directly to Anaconda cloud

To upload directly to a the Anaconda clound through your Anaconda username, run:

anaconda upload -u <ANACONDA USERNAME> <CONDA_TAR_BZ2>

To exit the docker container type exit

Licensing

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).

Contributing

We welcome contributions in the form of issue reports and pull requests.