Michelle Mendonca

The Archive and Package (arcp) URI scheme

Abstract The arcp URI scheme is introduced for location-independent identifiers to consume or reference hypermedia and linked data resources bundled inside a file archive, as well as to resolve archived resources within programmatic frameworks for Research Objects. Reference Stian Soiland-Reyes and Marcos Cáceres (2018): The Archive and Package (arcp) URI […]

GROmaρs: a GROMACS-based toolset to analyse density maps derived from molecular dynamics simulations

Abstract We introduce a computational toolset, named GROmaρs, to obtain and compare time-averaged density maps from molecular dynamics (MD) simulations. GROmaρs 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 […]