Force distribution analysis
The force distribution analysis (FDA) is a well-established tool for the calculation of time-resolved pairwise forces and stresses (http://dx.doi.org/10.1186/2046-1682-6-5). Please find a detailed documentation at https://github.com/HITS-MBM/gromacs-fda/blob/master-fda/fda-manual/fda-manual.pdf. At the moment, FDA is maintained in an extra GitHub repository https://github.com/HITS-MBM/gromacs-fda. We would like to integrate FDA into the official GROMACS repository.
FDA is using core functions of GROMACS calculating the pairwise forces during a md rerun process. Therefore, an extra binary (mdrun_fda) will be used, which extract the pairwise forces during the rerun process. To obtain a clean separation of FDA and GROMACS, the FDA version will only be built if the cmake flag 'GMX_BUILD_FDA' is switched on. If 'GMX_BUILD_FDA' is switched off, the unchanged GROMACS binaries will be built.
Activation of density fitting and move of module notifications
The densityfitting code is activated by adding it to the MDModules.
Moved the MdModuleNotifications to mdrunutility to break cyclic module
dependencies between mdrun and applied_forces via MdModules and
Observe that this patch changes the default .mdp output. Updated
reference data accordingly. Note that the changes in .mdp output
lead to "check mdp file differences" warning in the regression tests.