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So we can discuss it here:
``` py
from __future__ import print_function
from simtk.openmm import app
# TODO from constph import ConstpHForceField ?
import simtk.openmm as mm
from simtk import uni…
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I am trying to simulate a single Cosserat rod in MATLAB using your codes and the numerical scheme discussed in the following 2018 paper: https://doi.org/10.1098/rsos.171628. According to equations (C5…
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I did quick search on the docs and the github and I found that there wasn't much description of the constraint tolerance parameter. The most information I found was the docstring on Integrator (below…
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Solve the differential equation specified by Newton's 2nd law using the method of [Verlet integration](https://en.wikipedia.org/wiki/Verlet_integration)
Initial velocities should be assigned based …
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I wanted to restart the discussion about how we should best implement constant-pH methods into OpenMM, and most importantly, which layer this should be implemented into.
The best strategy is to combi…
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This issue is a roadmap for Molly.jl development. Feel free to discuss things here or submit a PR. Bear in mind that significant refactoring will probably occur as the package develops.
### Low han…
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Thanks for this, was looking to play around with SPH for ages and this makes it really convenient!
My plan is to create a self gravitating gas cloud, with as high a resolution as possible, but when…
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Copying from the alchemistry Slack channel from @davidlmobley:
We're having some issues with our work on binding mode sampling with NCMC (in BLUES), especially as we try to switch to the `AlchemicalN…
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The goal of this issue is to kickoff the discussion on the testing strategy. Hopefully we can unify names/concepts.
## **Our current testing landscape**
- E2E tests: they run a complete samplin…
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I'm discussing with @bas-rustenburg (the student heading up the constant-pH work) what setting up a constant-pH simulation should look like to the OpenMM user using the `app` layer. We'd like your in…