Comments (3)
Thanks for this!
If I understand this correctly, the first thing you are asking is for us to update the documentation. Do you have a suggested doc string? At first I was going to summarize the openmm doc and then include a link to it, but it sounds like even the openmm doc isn't great, so do you have a suggestion? Or, what would you like to see mentioned?
from openfe.
Yeah sorry this is all over the place; it'd be much easier if it was an OpenFE or OpenMM documentation issue and not a mixture of both
The best suggestion I've thought of would be a dressed-up version of
"""
Minimum distance from any solute atoms to the solvent box edge.
This argument is passed directly to OpenMM's addSolvent (link), which
typically produces boxes of size twice the padding distance plus the approximate
solute size, but for some small solutes may treat the solute as having zero size.
"""
This would communicate the quirk I'm observing in a way that squares the responsibility with OpenMM but doesn't assign blame. I think paraphrasing the OpenMM docs risks this docstrings falling out of sync each other, whereas just a link wouldn't be as useful to the OpenFE user. (If the behavior changes in OpenMM, this is a different issue altogether). That covers everything I have been thinking of, the most important thing being that it describes what happens
from openfe.
Thanks @mattwthompson. We could/should add it to this PR: #673, unfortunately it didn't make it into 1.0, but the ability to use the wider set of inputs from addSolvent alongside better docstring would be great.
from openfe.
Related Issues (20)
- Using other versions of small ligand ff (GAFF) instead of the default one HOT 1
- [CLI] inspect command for json output files
- Review zenodo authors
- CI fails with latest matplotlib
- 4-point water models fail with RBFE Protocol HOT 2
- `PersesAtomMapper` combined with minimal redundant networks can yield more than one edge/mapping connecting two ligands in a `LigandNetwork` HOT 5
- Gather should support result.json.gz HOT 1
- Questions about softcore potential for vdW and electrostatic interactions HOT 1
- Checkpoint restoration HOT 3
- Apparent convergence issues
- CI faiing with new OMMForceFields release
- Add conda canary
- Remove openmmforcefields 13 gaff test code branches
- `openfe.analysis.plotting.plot_2D_rmsd` does not work for fewer than 5 states
- Mypy fails
- Add support for GPU runners
- 2D RMSD plots are unreadable at high replica counts HOT 2
- 2D RMSD plots leave empty axes when state count is non-divisible by 4
- Cron CI is failing due to timeout
- Add setting indicating simulation is a vacuum state
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from openfe.