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As far as I can tell, there's no way to use sander to get single-point energies from a system with bond constraints and _not_ have a constraint algorithm applied. This is disappointing as single-point…
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I am using Foundation and have a grid of staff. Each staff member has a .memberitem class. Can I use HideSeek to filter that structure? Any examples?
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When I `M-x global-copilot-mode`, I run out of system memory.
It essentially spawns `.../copilot//dist/agent.js` processes until the OOM starts killing off programs.
Annoyingly, for some reason…
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I've managed to reproduce this on a minimal setup, loading only `typescript-mode` (which activates `electric-indent-mode`, `copilot.el` (latest HEAD, 2c1c425).
https://asciinema.org/a/7j1X1KGr85Nl6…
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The output of `deepCL/backproweights.cl` can be improved by enhacement of reducing the number of `ldi`.
For example, loading constant `256` happens 69 times.
If we can combine them to one instructi…
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**Describe the bug**
loading MD lammps cg spica trajectory gives error and does not load.
**To Reproduce**
Topology: 4ypg-e.psf
Trajectory: 4ypg-20fs.lammpsdump
"Load"
**Expected behavior**
…
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I'm getting different angle energies for a simple single-molecule system.
Reproduction
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Unzip these files: [repro.zip](https://github.com/openforcefield/openff-interchange/files/6…
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OpenFF's mainline force fields use a 9 A cutoff for vdW interactions. Code paths involving `openmmforcefields` do not, by default, use this cutoff and instead fall back to the default of 1 nm:
```p…
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It would be helpful to have a convenience function on the force field object which allows us to find (or extract) force field parameters or nodes in general which have certain cosmetic attributes atta…
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Has this been tested with OPC water. I keep getting
AmberWarning: Molecule atoms are not contiguous! Attempting to reorder to fix.
warn('Molecule atoms are not contiguous! Attempting to reorder…