Comments (2)
Will take a closer look tomorrow, but in passing these all look like good ideas
hybrid functional form
I forget if there was a good reason for doing this ... I think this was motivated by needing to get one of the torsion styles to match up, but I don't remember if this means the bond style must also be the cursed hybrid style. Certainly only harmonic bond stretching is supported now. Pretty annoying re: restart files!
Atoms # full
I didn't know about this trick - seems funky to encode this information after a pound, but also potentially useful! It looks like there are several sections this could apply to? https://docs.lammps.org/read_data.html#format-of-the-body-of-a-data-file
The "atom/bond/etc count" section format has changed
No dog in the fight, but is the ordering implied by some sort of community understanding or other tool? You're right that LAMMPS itself does not care ("Header lines can come in any order.")
it handles things better if the 'tilt' section is not included if all zeros
Should be an easy patch - check if this condition is met, then don't print that stuff
I'd be happy to review/co-author PRs from Tim or others on any of these. Preferably separate PRs for each, and it looks like the list top-to-bottom is ordered in descending scope/difficulty.
from openff-interchange.
Related Issues (20)
- Wrong "scale_14" read from .json file HOT 5
- "dOH" written incorrectly in `[ settles ]` section HOT 2
- How to check missing parameters before create_interchange? HOT 2
- Pass cosmetic attrs through to `Potential` objects HOT 3
- Missing v-site exceptions with plugins HOT 5
- `Interchange.from_openmm` should raise an exception if the topology doesn't match the system HOT 3
- ligand always out of box in ligand_in_water.ipynb HOT 4
- Update GROMACS portion of ligand example
- Loading topologies from OpenMM sometimes scrambles atom order HOT 2
- Electrostatics key mismatch after combination HOT 3
- Positions of `MonovalentLonePair` virtual sites is incorrect (does not affect simulations) HOT 1
- Virtual site parameters can clash if looked up using only SMIRKS HOT 4
- `experimental/openmmforcefields/gaff.ipynb` and `ligand_in_water.ipynb` notebooks broken on OpenFF Docs HOT 1
- units for `Interchange.collection['Bonds'].get_system_parameters()` HOT 2
- Support GROMACS's `3fad` virtual sites
- `get_positions_with_virtual_sites` does not collate virtual sites with molecules HOT 1
- Some combinations of Interchanges do not commute HOT 2
- LAMMPS versions prior to 2023.08.02 are incompatible with Interchange, but may be installed with it HOT 2
- Interchange.to_gromacs() creates a topology with far too many atomtypes, which influences GROMACS performance HOT 4
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 openff-interchange.