Niels Kristian Kjærgård Madsen

Missing unsigned integer => floating-point conversions

1

The current implementation of `ConvertTo` does not have an overload for unsigned integer to floating-point conversion. For my specific application I need to convert uint32 => float32 and uint64 =>...

ALPB solvation model with salt screening.

4

**Describe the bug** When running GFN2-xTB calculations with ALPB the energy does not converge to the zero-ion-strength limit. **To Reproduce** Try to run energy calculations with the Still kernel (the...

NaN propagation in exponential function

4

When applying the `Exp` function to `NaN` on my CPU (Intel i7-1185G7 using the AVX3_DL target) the function returns `0.0` instead of the `NaN` that I expected (and that `std::exp`...

`AssignBondOrdersFromTemplate` does not copy bond stereochemistry information of terminal imine

1

[terminal-imine.pdb.txt](https://github.com/rdkit/rdkit/files/13278105/terminal-imine.pdb.txt) Assigning bond orders to the attached PDB with SMILES:` [H]/N=C\CC(=O)N1CC[C@@H](C)[C@@H](N(C)c2ncnc3[nH]ccc23)C1` removes the stereochemistry of the C=N bond in the terminal imine group. **To Reproduce** ``` from rdkit.Chem import AddHs,...

Reuse of GFN-FF topology in ONIOM calculations

1

Is it possible to reuse the GFN-FF topology between ONIOM calculations on a large system, where GFN-FF is used as low-precision method? I have tried to run the same calculation...

Overflow errors with random seeds

5

Calling `LangevinMiddleIntegrator.setRandomNumberSeed` or `Context.setVelocitiesToTemperature` sometimes fails with an overflow error when using a `numpy.uint32` genereted by e.g. a `numpy.random.SeedSequence`. The C++ signature also states that the argument should be a...

Documentation lacks information on default pressure unit

1

The table in [section 18.2](http://docs.openmm.org/latest/userguide/theory/01_introduction.html#units) of the documentation does not contain the default unit of pressure used in OpenMM. This could be valuable information when e.g. updating the pressure using...

Failing energy minimization

6

[2wpa.pdb.txt](https://github.com/openmm/openmm/files/13319836/2wpa.pdb.txt) The following energy minimization ends at a state with max. absolute force element = 7.6e7 kJ/mol/nm. When I use my own implementation of the FIRE algorithm for optimizing the...

findMissingAtoms raises AttributeError if findMissingResidues has not been called first

1

The following code raises `AttributeError: 'PDBFixer' object has no attribute 'missingResidues'`: ``` from pdbfixer import PDBFixer fixer = PDBFixer("6dyo.pdb") fixer.findMissingAtoms() ``` Using the PDB from https://www.rcsb.org/structure/6DYO

Question on the nonbonded cutoff implementation for implicit solvent models

6

In the current version of `customgbforces.py` all GB models implement the nonbonded cutoff by subtracting `1/cutoff` from the `1/f` factor. This is of course negative if `f > cutoff`, and...