Introduction

Force Distribution (FDA) is implemented in the Gromacs version (4.0.5). The code has been tested on a wide range of machines and systems, but the authors cannot take any warranty or guarantee for the correctness of the results. As all code within Gromacs, this code is published under the GPL v2, and thus is freely available and re-distributable.

Additionals, data analysis

The FDA-output files are binary, which saves space and allows for fast import / export. To make these files easily accessible by the user, the FDA code comes with an R-package that provides functionality to import and analyze pair-wise forces directly in R (R, a language for statistical computing and is available free of charge). In case you want to use a different software package we also provide a Gromacs tool to convert binary into ASCII files.

Please see the FDA-manual in the download area for details.

Download and installation

Installation works identical to the standard Gromacs release. Check the Gromacs website for details. The FDA code is an extension, and as one would expect nothing will change if you are running your MD simulations using FDA-Gromacs. In fact the FDA code will not be called unless you explicitly tell Gromacs to do so.

Installing the FDAtools package

FDAtools depends on bio3d and SparsM. Please download the bio3d package. A a Mac / Linux user, check that your R_LIBS variable points to the folder in which packages should be installed (insert an export R_LIBS="..." in your .profile / .bashrc if not previously done). Install bio3d by executing 'R CMD INSTALL bio3d_1.0-6.tar.gz'. Install SparseM by executing 'install.packages("SparseM")' in an R console. Now we are ready to install FDAtools, just type 'R CMD INSTALL FDAtools_1.0.tar.gz' on the command line.

Documentation

The following documentation is available

• Force Distribution Analysis with Gromacs in the downloads section
• tutorial files - force trajectories and structure files used in the tutorial
• R package documentation for the FDAtools package

The manual contains user specific as well as implementation specific details. I.e it contains a detailed description of the binary file format that should allow to implement your own methods working on these files.

There are several publications based on force distribution analysis (see below). If you are not familiar with FDA at all this is a good point to start reading!

Citation

If you are using force distribution analysis, please cite this article:

http://dx.doi.org/10.1186/1471-2105-12-101