"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. An RNA molecule on the water surface. The isosufrace of the density of a cationic lipd colored by the density of cholesterol.

Project Activity

See All Activity >

Categories

Data Analytics

Follow Grid3D Toolbox

Grid3D Toolbox Web Site

Other Useful Business Software
Secure User Management, Made Simple | Frontegg Icon
Secure User Management, Made Simple | Frontegg

Get 7,500 MAUs, 50 tenants, and 5 SSOs free – integrated into your app with just a few lines of code.

Frontegg powers modern businesses with a user management platform that’s fast to deploy and built to scale. Embed SSO, multi-tenancy, and a customer-facing admin portal using robust SDKs and APIs – no complex setup required. Designed for the Product-Led Growth era, it simplifies setup, secures your users, and frees your team to innovate. From startups to enterprises, Frontegg delivers enterprise-grade tools at zero cost to start. Kick off today.
Start for Free
Rate This Project
Login To Rate This Project

User Reviews

Be the first to post a review of Grid3D Toolbox!

Additional Project Details

Registered

2014-01-20
Report inappropriate content