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PyBrella

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Python script to automate umbrella sampling with AMBER

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Description

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

PyBrella Web Site

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.

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Additional Project Details

Intended Audience

Science/Research

Programming Language

Python

Registered

2013-08-07

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