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Updated readme and license, cleaning up unneeded files.

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Niels Müller
2017-11-14 12:39:29 +01:00
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README.md
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# Pygmx
A Cython wrapper for the shared library of GROMACS 5.1.
A Cython wrapper for the shared library of GROMACS 2016
## Installation
Pygmx requires some python packages and an installation of GROMACS 5.1.
Pygmx requires some python packages and an installation of GROMACS 2016.
### Python requirements
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### Gromacs installation
Pygmx requires the shared library and header files of Gromacs 5.1 or higher to be installed.
Note that pygmx also supports the Gromacs-2016 version.
Checkout the followng git branch if this version of Gromacs is desired:
git checkout gromacs-2016
Note that Gromacs is backwards compatible, i. e. files produced by the 5.1 version will also work in the 2016 version.
But Gromacs-2016 is required to load files of the 2016 version.
#### Using a module
If gromacs is installed as a module in your system, run
module load gromacs/5.1
and skip to the section *Installing pygmx*.
Note that on the AG Vogel intranet pygmx is available through the module `mdevaluate`.
Pygmx requires the shared library and header files of Gromacs 2016 to be installed.
#### Through package manager
On many Unix distributions Gromacs may be installed through the package manager.
On many Unix distributions, Gromacs may be installed through the package manager.
The required packages, which provide the headers, are usually named `gromacs-devel` or `gromcas-dev`.
#### Manual build
To build the shared library manually, follow the [official installation instructions](http://manual.gromacs.org/documentation/5.1.2/install-guide/index.html).
To build the shared library manually, follow the [official installation instructions](http://manual.gromacs.org/documentation/2016.4/install-guide/index.html).
Make sure to source the `GMXRC` script, which sets the environment variable `LD_LIBRARY_PATH` to the correct location or set this variable manually.
Don't bother with advanced features like GPU support if the Gromacs installation will only be used for pygmx,
since the file io functions do not use these features.
### Installing pygmx
When the requirements are met, the installation should be easy.
Navigate to the top folder of the repository and run the command
When the requirements are met, installing pygmx into the local Python installation can be achieved by navigating to the top folder of the repository and running the command
python setup.py install
This builds the cython modules and installs them into the local python distribution.
To check if everyting works run
To check if everyting works, run the following command from a directory out of the repository
python -c 'import pygmx'
If this raises an error that refers to `libgromacs.so`, this means the Gromacs library could not be found.
If this raises an error that refers to `libgromacs.so`, the Gromacs library could not be found.
Make sure it is either in a standard location or `LD_LIBRARY_PATH` is set correctly.