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- relevant for cases in which a close contact for one central atom is desired
- if vdW radii are partially not perfectly suited for this approach, they could be corrected
- could be applied to the v…
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Hi,
I have been working on setting up Atomate2 for my VASP calculations, and I encountered an issue related to the VASP_VDW_KERNEL_DIR variable. I followed the instructions provided in the Atomate2…
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Good evening,
We have completed all the tests described in the manual to ensure that Mobcal was installed and compiled correctly. The results we obtained matched those you provided.
Additionally…
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following generated code and causes linter error:
```
typedObj !== null &&
typeof typedObj === 'object' ||
typeof typedObj === 'function'
```
`ESLint: Unexpected mix of '&&' and …
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Dear lightdock developers
First of all, thank you for developing lightdock and lightdock-rust.
I'm a little new to lightdock. I want to add modified nucleic acids to the amber DNA scoring functi…
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`maxfev` being so large is likely an indication that logistic curves are a poor fit.
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**Describe the bug**
When optimizing molecule conformers using UFF, sometimes the lowest energy conformer has 2 H atoms in (nearly) identical positions. The UFF energy for this conformer can be lower…
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The `_ATOMIC_RADII` dictionary here (https://github.com/mdtraj/mdtraj/blob/master/mdtraj/geometry/sasa.py) is missing some canonical atoms that are processed by MDTraj normally in other ways, such as …
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The electrostatic and vdW calculations do not currently work in FDBM, as you can test e.g. with the `ppafm/examples/pyridineDensOverlap/` example.
Running `ppafm-generate-elff -i sample/LOCPOT.xsf …
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Dear OpenFE team developers,
`
def _nonbonded_custom(self, v2):
"""
Get a part of the nonbonded energy expression when there is no cutoff.
Returns
-------
…