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