PyBrella

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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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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