Grabe lab related software

 
 
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ABPSmem

An easy-to-use interface for carrying out electrostatics calculations on membrane proteins using the software APBS as a backend solver. APBSmem can be downloaded here, and APBS can be found here.

WESTPA

WESTPA (The Weighted Ensemble Simulation Toolkit with Parallelization and Analysis) is a high-performance Python framework for carrying out extended-timescale simulations of rare events with rigorous kinetics using the weighted ensemble algorithm. The software includes (1) options for further enhancing the sampling efficiency through reassignment of weights according to either equilibrium or nonequilibrium steady state, and (2) plugins for using a weighted ensemble-based string method and the WExplore method.

Berkeley Madonna

Berkeley Madonna is a piece of software designed to easily set up and solve ordinary differential equations in the mathematical and physical sciences. It was developed by Drs. Bob Macey and George Oster at UC Berkeley, and it is used widely in both professional settings and as a tool for undergraduate teaching.