New interface for dynamic access to atom properties during GROMACS simulations


This mini project adds infrastructure to GROMACS to support new kinds of simulations, guided by restraints derived from other data such as Cryo-EM, and/or retrospectively observing how well simulations conform with such data (when not guided).

Though Cryo-EM data is being used here to evaluate the technique, the infrastructure for efficiently retrieving atom information during simulation runtime will be applicable to any type of external input about a system, from small-angle x-ray scattering (SAXS) and small-angle neutron scattering (SANS) to secondary structure information, etc. The code is already being used (in alpha-testing) researchers from Polytechnical University of Gdansk.