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**Describe the bug**
I'm not sure if this is a bug or if the code is working as intended, but the time it takes to write each MD frame is taking significantly longer than any other part of the simula…
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Action items:
- [x] @bbefort prototype class to generalize `PR_model` for the cases, place in same folder as current semi-generalized functions (`linear`, `cubic`)
- [x] @jialuw96 demonstrate Pyomo.…
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**Describe the bug**
A `ForceField` with no `Electrostatics` tag can be used to create an OpenMM `System` with arbitrarily-set electrostatics.
**To Reproduce**
```
from openforcefield.typing.e…
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Dear developers of SPARC:
There's no any tags about VDW in your manual file, so can it be used to calculate Van der Waals materials?
jyli
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Add the analysis of converging fraction R_c from the paper
S. Fan, B. I. Iorga, and O. Beckstein. Prediction of octanol-water partition coefficients for the SAMPL6- log P molecules using molecula…
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Binding energies between ligand and receptor should be computed relative to the receptor's internal binding energies. Before docking the ligand, the entire receptor, or at least the binding pocket, sh…
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As described in the title, by setting `vdw_method d2`, the geometry relaxation can not converge. The `LARGEST GRAD` would just diverge:
```
>grep "LARGEST GRAD" out.m
LARGEST GRAD (eV/A) : 4.45…
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Set up meeting with stakeholders to determine how we should use the "Received Items" if inventory planners will be involved in the process and show proposed enhancements.
# 7/27
Talked to AMD sta…
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Hi,
If I add an octahedral solvent box to the attached protein ([input_protein.pdb.txt](https://github.com/openmm/openmm/files/9082148/input_protein.pdb.txt)), I end up with a large number of wate…
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Some meshes come out with artifacts. Often, the molecular surfaces (VdW, SES, SAS) are smoothed with Laplacian smoothing, e.g.
- Taubin paper: https://graphics.stanford.edu/courses/cs468-01-fall/Pa…