Brownian Elastic Networks with Dynamic Topology
Copyright ©2023- Tomasz Skóra tskora@sci.utah.edu
Warning
The software is not extensively tested yet! It's just a prototype!
- Brownian dynamics w/o hydrodynamic interactions
- customizable atom-atom (2-body) interactions
- customizable many-body interactions
- customizable event-driven bond topology changes
- [] input/output handling
To install, type following commands in a terminal:
$ pip3 install pybendt| Physical property | Units |
|---|---|
| Temperature | kelvin (K) |
| Friction coefficient | picosecond times kilocalorie per mole per angstrom squared (ps kcal/mol/Å^2) |
| Time | picosecond (ps) |
| Distance | angstrom (Å) |
| Energy | kilocalorie per mole (kcal/mol) |
| Force | kilocalorie per mole per angstrom (kcal/mol/Å) |
| Force constant | kilocalorie per mole per angstrom squared (kcal/mol/Å^2) |
Note
There is a separate function
friction_from_hydrodynamic_radius_and_viscositywhich takes hydrodynamic radius in angstrom (Å) and viscosity in centipoise (cP) and returns friction coeffiient in picosecond times kilocalorie per mole per angstrom squared (ps kcal/mol/Å^2).
The following people contributed to the development of pybendt.
- Tomasz Skóra -- creator, lead developer (contact: tskora@sci.utah.edu)