pybendt 0.0.3

Brownian Elastic Networks with Dynamic Topology

pybendt

Brownian Elastic Networks with Dynamic Topology.

Copyright ©2023- Tomasz Skóra [e-mail]

Warning

The software is not extensively tested yet! It's just a prototype!

Features

• Brownian dynamics w/o hydrodynamic interactions
• customizable atom-atom (2-body) interactions
• customizable many-body interactions
• customizable event-driven bond topology changes

Quick start

To install, type following commands in a terminal:

$ pip3 install pybendt

Units

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_viscosity which 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).

Authors

The following people contributed to the development of pybendt.

• Tomasz Skóra -- creator, lead developer (contact: [e-mail])