Welcome! Glad you intend to use ReaDDy for your particle-based reaction-diffusion simulations. This is a quick starting package that sets you up right away.
Run a simulation right away:
- go into simulation folder
cd sim
- run the simulation
./run.sh
Look at the simulation
- download VMD:
// if you are on a mac: open the .tcl script differently: Open VMD, click on 'File' in the upper left corner of the screen, click 'source' in the dropdown menu, and choose the StarterKitPath/sim/output/out_traj.xml.VMD.tcl to view it.
- have a look at your simulation trajectory:
vmd -e output/out_traj.xml.VMD.tcl
// The _bin_VMD-Visualizer automatically creates a vmd readable xyz trajectory from the readdy xml output and provides a VMD .tcl script to view it right away
Change the simulation parameters:
You will find all simulation parameters in
cd input