GROMACS

Within BioExcel project we are tasked to develop a new QM/MM interface between GROMACS and CPMD. The new interface is done using Multiple-Program Multiple-Data approach. Within this strategy both CPMD and GROMACS are running in parallel independently. GROMACS is used as an MM force provider in this framework. In the beginning of a timestep GROMACS receives the set of coordinates, computes forces and potential energy and sends them to CPMD. CPMD is handling the QM forces as well as the integration and thermostats.

In order to achieve that a number of things has to be done:

1. Zero charges in the QM region of GROMACS (to avoid double-counting of electrostatics)
2. Remove LJ interactions between QM atoms (modification of exclusion lists)

This would require the modification of the GROMACS preprocessor to zero charges and modify intra-molecular exclusion lists.
Moreover, additional changes in core GROMACS are required. First, we need to implement inter-molecular exclusions of non-bonded interactions of QM atoms with QM atoms. Then, additional work is needed to implement the MiMiC protocol (see attached pdf document)