https://github.com/readdy/readdy-sim-starterkit
This starter kit contains templates and necessary binaries to start simulating right away.
https://github.com/readdy/readdy-sim-starterkit
Last synced: 4 days ago
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This starter kit contains templates and necessary binaries to start simulating right away.
- Host: GitHub
- URL: https://github.com/readdy/readdy-sim-starterkit
- Owner: readdy
- Created: 2014-07-31T07:18:06.000Z (almost 12 years ago)
- Default Branch: master
- Last Pushed: 2014-08-22T07:58:15.000Z (almost 12 years ago)
- Last Synced: 2025-02-27T12:45:14.895Z (over 1 year ago)
- Language: Shell
- Size: 1.35 MB
- Stars: 3
- Watchers: 5
- Forks: 1
- Open Issues: 0
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Metadata Files:
- Readme: README.md
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README
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:
1) go into simulation folder
> cd sim
2) run the simulation
> ./run.sh
Look at the simulation
1) download VMD:
> http://www.ks.uiuc.edu/Research/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.
2) 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