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This is an effect of how [(upstream bug 4051)](https://gitlab.com/gromacs/gromacs/-/issues/4051) is being handled. However, this also means that there is a slightly problem of excluded atoms interacti…
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**Description**
[NADP](https://en.wikipedia.org/wiki/Nicotinamide_adenine_dinucleotide_phosphate) (SMILES `"c1cc(c[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)([O-])O[P@](=O)(O)OC[C@@H]3[C@H]([C…
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I found that even if they are all pdb files, some can be displayed, some can not.
1. When I run the local DhaA80_0001.pdb file, I can display the result, and the file looks like this.
HEADER …
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When parsing a geometry with atoms for which there are no covalent radii, the program will crash.
Here is an example with the xyz attached:
```
geom = berny.geomlib.readfile("xtb.xyz")
intcoords…
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The workflow we've been using with OPLS doesn't work for most forcefields. In Amber, for example, non-bonded VdW and bonded interactions are specified through atomtyping but partial charges are assign…
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Nota: ¿sólo pasa en la consola?
Cuando la representación es Bonds, y se introduce en la consola el comando
> select 0:0:A
se genera el siguiente error en el navegador:
```
Uncaught TypeErro…
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**Description**
to_inpcrd writes a time of 0.0
**Reproduction**
```
`
from openff.toolkit import ForceField, Molecule, Topology
from openff.units import Quantity, unit
from openff.inter…
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Would it be possible to add examples (ideally for multidimensional df) to the documentation of alchemlyb.preprocessing.subsampling?
At least I am not able to guess the usage of statistical_inefficien…
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Hi @vdw,
In one project, I wanted to show only the first 5 elements of a list. Therefore, the hidden_mode was not suitable and here is what I did: `$('#adh-other-lamps>li:not(:lt(5))').hide();`.
But…
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I started adding support for PySCF in my D3 reimplementation, see https://dftd3.readthedocs.io/en/latest/api/pyscf.html. However, I'm not really a PySCF user and not 100% sure whether this implementat…