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smog-server / OpenSMOG

OpenSMOG is a Python library for performing molecular dynamics simulations using Structure-Based Models. OpenSMOG uses OpenMM.
MIT License
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add minimization #42

Closed Whitford closed 2 years ago

Whitford commented 2 years ago

In the short-term, we need to, at least, give an example of how to use energy minimization. While pure SBMs don't need it, many people will (e.g. all of the amber-bonds variants). In the long-term, it would be worth adding a wrapper for energy minimization, so that it is intuitive.

Whitford commented 2 years ago

This wrapper is now included. There was an issue where minimization would overwrite the initialized velocities. As a result, if one minimized and immediately performed a simulation, the run would typically crash. Now, the minimize routine always resets the velocities, after minimization completes.

Usage of minimize is now documented in the help() routines, but it is not documented on the webpage.