GROmaps

Density maps from atomic positions using GROmaps. For MD trajectories, the density map is time averaged over an ensemble of positions sampled by the group of atoms.

GROmaρs is an open-source GROMACS-based toolset for the calculation and comparison of density maps from molecular dynamics simulations.

GROmaρs is developed to obtain and compare time-averaged density maps from molecular dynamics simulations. GROmaρs efficiently computes density maps by fast multi-Gaussian spreading of atomic densities onto a three-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.

This is especially advantageous for multimolecule systems in which standard comparisons like RMSDs are difficult to compute.

Resources

You can find information how to download, install, and execute the toolset, here.

R Briones, C Blau, C Kutzner, BL de Groot, and C Aponte-Santamaría
GROmaρs: a GROMACS-based toolset to analyse density maps derived from molecular dynamics simulations
Biophysical Journal. 116: 4-11 (2019)
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