SimFRET is a Python package to simulate FRET experiments. The program allows running a quick simulation using the SMOG potential and to give suggestions about pairs of residues for FRET dye attachment. Giving the structure files of target macromolecule, the program automatically overlaps the dyes and computes the FRET efficiency. In the link below you can find the program and website for task submission:
SimFRET
CryoFit
CryoFit is a program that fits biomolecules (protein and nucleic acids) to Cryo-EM map which is reconstructed by single particle analysis using MD simulation. A widely used MD simulation package, Gromacs program, is integrated to one of the most popular structural biology programs, Phenix, to allow physics based refinement in a fast and user-friendly way. In the link below you can find the program and tutorial:
https://www.phenix-online.org/documentation/reference/cryo_fit.html