Grid3D Toolbox

"Grid3D Toolbox" is a set of command line tools for visualization and analysis of the results of molecular simulations based on 3-dimensional density maps (grids). Currently, the tools only work with the simulation trajectories generated by the GROMACS simulation package (http://www.gromacs.org/).

The generated density maps are saved in the Grid3D native .g3d format and can be visualized using a third party data visualization software. A converter from the .g3d format to .vti, an XML based format of the VTK library is provided with the "Grid3D Toolbox", so that the generated density maps can be visualized using the ParaView data analysis and visualization software (http://www.paraview.org).

For more details read the upcoming publication in Faraday Discussions:
FD169: Density based visualization for molecular simulation.

Project Samples

Density based representation of a lipid nano-particle. Shown as a scross-sectional slab in ParaView.

RNA molecules inside a lipid nano-particle on water intefaces. Shown by isosurfaces of the RNA and water densities.

The external interface of a nano-particle shown as an isosurface of the water density in the system.

$The internal cavities inside a nano-particle shown by a semi-transparent isosufrace of water density.$

$The isosufrace of the density of a cationic lipd colored by the density of cholesterol.$

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Additional Project Details

Registered

2014-01-20

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