GROma?s: a GROMACS-based toolset to analyse density maps derived from molecular dynamics simulations (Biophysical Journal)

We introduce a computational toolset, named GROma?s, to obtain and compare time-averaged density maps from molecular dynamics (MD) simulations. GROma?s efficiently computes density maps, by fast multi-Gaussian spreading of atomic densities onto a 3-dimensional grid. It complements existing map-based tools by enabling spatial inspection of atomic average localization during the simulations. Most importantly, it allows the comparison between computed and reference maps (e.g. experimental), through calculation of difference maps, and local and time-resolved global correlation.