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wiederm / endstate_correction

Endstate corrections from MM to QML potential
https://wiederm.github.io/endstate_correction/
MIT License
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clean up code #62

Closed wiederm closed 1 year ago

wiederm commented 1 year ago

Description

This PR updates some of the legacy code that has been part of this repository as a result of some ad hoc decisions during the begging of the project.

Specifically, (1) we are now using the dedicated DCDReporter for saving trajectories, (2) handle the system generation outside of the package and only generate the simulation instance, (3) automatically detect the fastest platform, (4) remove functions for velocity seeding (now use the openMM functionality for that)

Status

wiederm commented 1 year ago

tests are passing locally

wiederm commented 1 year ago

Thanks, @xiki-tempula for your input. I agree that this PR should have been split into multiple, smaller PRs. The process here was a bit rushed and doesn't complelty reflect best practices.