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

See All Activity >

License

GNU General Public License version 3.0 (GPLv3)

Follow PyBrella

PyBrella Web Site

Other Useful Business Software

Gen AI apps are built with MongoDB Atlas

Build gen AI apps with an all-in-one modern database: MongoDB Atlas

MongoDB Atlas provides built-in vector search and a flexible document model so developers can build, scale, and run gen AI apps without stitching together multiple databases. From LLM integration to semantic search, Atlas simplifies your AI architecture—and it’s free to get started.

Start Free

Rate This Project

User Reviews

Be the first to post a review of PyBrella!

Additional Project Details

Operating Systems

BSD, Linux

Intended Audience

Science/Research

Programming Language

Python

Related Categories

Python Molecular Mechanics Software

Registered

2013-08-07

Similar Business Software

Ascalaph Designer

Ascalaph Designer is a general-purpose program for molecular dynamic simulations. Under a single graphical environment are represented as their own implementation of molecular dynamics as well as the methods of classical and quantum mechanics of popular programs. Molecular geometry optimization...

See Software
YASARA

YASARA is a molecular graphics, modeling, and simulation program for Windows, Linux, MacOS, and Android developed in 1993, that finally makes it really easy to answer your questions. With an intuitive user interface, photorealistic graphics, and support for affordable virtual reality headsets,...

See Software
ArgusLab

ArgusLab is a molecular modeling, graphics, and drug design program for Windows operating systems. It’s getting a little dated by now, but remains surprisingly popular. To date, there are more than 20,000 downloads. ArgusLab is freely licensed. You don’t need to sign anything. You can use as...

See Software
Promethium

Promethium is a GPU-powered chemistry simulation platform designed to accelerate drug and materials development by enabling faster and more accurate quantum chemistry calculations. Built from the ground up for NVIDIA datacenter GPUs like A100, it employs novel QC Ware streaming algorithms to...

See Software
MolView

MolView is an intuitive, Open-Source web application to make science and education more awesome! MolView is mainly intended as a web-based data visualization platform. You can use MolView to search through different scientific databases including compound databases, protein databases and...

See Software
ChemDoodle

ChemDoodle 2D contains thousands of chemistry features, helping you produce the highest quality graphics and saving you hours of work. We spend a very long time scrutinizing the graphics output in ChemDoodle. The software automatically orients bonds in the correct directions, merges bond strokes...

See Software