PyBrella is a script designed to automate the umbrella sampling process, using the AMBER molecular dynamics package.

Features

  • Automates the setup and execution of MD runs for umbrella sampling on the distance parameter, using user-defined start- and endpoints.
  • Performs confirmation of sample convergence based on the 80/20 chi-squared distance method.
  • Examines the sample histograms and automatically begins new samples where necessary to reach a specified sampling threshold.

Project Activity

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Categories

Molecular Mechanics

License

GNU General Public License version 3.0 (GPLv3)

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Additional Project Details

Operating Systems

BSD, Linux

Intended Audience

Science/Research

Programming Language

Python

Related Categories

Python Molecular Mechanics Software

Registered

2013-08-07
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