This is the Linux app named PyBrella whose latest release can be downloaded as pybrella.py. It can be run online in the free hosting provider OnWorks for workstations.
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PyBrella
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DESCRIPTION
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.
Audience
Science/Research
Programming Language
Python
Categories
This is an application that can also be fetched from https://sourceforge.net/projects/pybrella/. It has been hosted in OnWorks in order to be run online in an easiest way from one of our free Operative Systems.