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For the case of using DFT for [openff-bespokefit](https://github.com/openforcefield/openff-bespokefit) the step of `enerating bespoke QC data` is quite slow and I think this could be more verbose.
I …
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When writing links, you could do e.g.
```
[ link ]
resname $dna_resnames
[ angles ]
BB1 BB2 +BB 2 bb1_bb2_bb {"group": "Backbone linking angles"}
[ dihedrals ]
BB1 BB2 +BB +BB1 2 bb1_bb2_bb_b…
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Dipeptide dihedral energies are slightly off (around `0.01` to `0.02` kcal/mol). Doesn't appear to be a parameter mismatch. Unsure about root cause, since dihedrals are being set to match AMBER order.…
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Hi, Great Work! Could you please tell me the reason of subtracting the angle loss and the dihedral loss (at the bottom of code)? Thank U~
` def batch_molecule_loss(self, true_stats, model_stats, i…
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We've made a lot of improvements in how we handle errors on reading input files, but we still need to get better. This simulation returns an error:
`Reading from CHARMM-Style parameter file: …
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I load a Amber prmtop file as Parmed Structure
Then I convert all DihedralType to DihedralTypeList
I can save the the Structure as gromacs top file with correct dihedral function type 9
However, W…
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As discussed on the dev mailing list, we should have a method that calculates all possible distances, angles, dihedrals, etc.
Possibly useful references:
* https://github.com/CrawfordGroup/Program…
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hi
I am trying to convert a lammps data files to gromacs gro file by intermol, but I got the following error:
' File "C:\Users\ALW\AppData\Local\Packages\PythonSoftwareFoundation.Python.3.8_qbz5…
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@jpthompson17 mentioned a neat idea that should simplify the dihedral logic.
Every dihedral (and perhaps other forces later down the road) should know how to convert itself to the canonical form. Thi…
ctk3b updated
8 years ago
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Hi, wonderful work!
I wonder if the mols generated follow the same angle distribution and dihedral angel distribution with real mols.