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Python / C++ based particle reaction-diffusion simulator
lightweight hdf5 wrapper
Example notebooks to demonstrate the usage of readdy
This library allows to do particle-based reaction-diffusion simulations.
This starter kit contains templates and necessary binaries to start simulating right away.
The readdy-input-topology-generator (Topology Generator) creates input topology files for particles and groups, given a file how many particle and how many groups are desired and on which geometry (i.e. potentials) these particles/groups should reside.
This tool parses ReaDDy output trajectories and creates an VMD readable output and a VMD .tcl script to visualize it.