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Create nonequilibrium multi state sampler

1

We want to create a `NonequilibriumMultiStateSampler` that takes in 2 states (and optionally 2 auxiliary states with LRC fully on) and run nonequilibrium switching. The class should optionally accept rest...

zhang-ivy

Add gentle equilibration code

1

I recently implemented the gentle equilibration protocol from [this publication](https://academic.oup.com/nar/article/44/1/63/2499624#supplementary-data) in OpenMM: ```python from openmm import unit import pickle import argparse import logging # Set up logger _logger = logging.getLogger()...

zhang-ivy

MultistateSampler - make iteration logging info level instead of debug?

1

Discussing things with @mikemhenry today, it would be quite useful if we could get a general sense of run progression for MultistateSampler derived classes without getting all the debug information...

IAlibay

## Description I couldn't see anywhere where the effective length of the data was exposed so I added it. I couldn't see where the other similar properties were tested, so...

richardjgowers

From working in #593 it was noted that we need better testing for the offline analysis and MBAR estimates that end up in the real time analysis file.

ijpulidos

Update to MolSSI cookiecutter

3

We should restructure the repo to be consistent with the [MolSSI CMS cookiecutter](https://github.com/MolSSI/cookiecutter-cms).

jchodera

I think adding (and making sure we are happy with) the changelog entry as part of the template will: 1) Improve the quality of the change log entry, since that...

mikemhenry

Enhance stability of minimization

6

## Description I have been experiencing some instabilities which, after much difficulty, I was able to track down to the minimizer. The observed behavior is that the minimizer will finish...

jfennick

Accessing context during ReplicaExchange

2

I am attempting to run Replica Exchange for a system and would ideally like to access the context during the course of the simulation run in order to extract the...

clarktemple03

Demultiplexing RepEx trajectories

6

Hi, I'd like to use openmmtools's replica exchange code, but I can't see a way of actually demultiplexing the trajectories and having a look at them. Am I missing something?...

dlukauskis