Selim Sami

Custom virtual sites

35

Hi, Is there a way to add custom virtual site equations, just like you add custom forces? If not, could you point out which parts of the code I would...

Charge flux in openmm

3

Hi, I'd like to use charge flux model as implemented for AMOEBA in the FF that I am working on. Is this implemented in OpenMM? That's the impression I got...

**Describe the bug** GFN-FF does not compute the electrostatic potential and ignores the --esp flag, while the flags works fine with the gfn1 or gfn2. **To Reproduce** xtb coords.xyz --gfnff...

Metadynamics keyword "atoms" is not recognized

3

**Describe the bug** Metadynamics keyword "atoms" is not recognized. This is supposed to apply the RMSD bias to only a selection of atoms **To Reproduce** Steps to reproduce the behaviour:...

Adding NBFix like corrections to the ForceField object

6

``` ff = ForceField("amber/protein.ff14SB.xml", "amber/tip3p_standard.xml") mol_lig = Molecule.from_file('molecule.sdf', allow_undefined_stereo=True) smirnoff = SMIRNOFFTemplateGenerator(mol_lig, allow_undefined_stereo=True, forcefield="openff-2.0.0.offxml") ff.registerTemplateGenerator(smirnoff.generator) ``` If I want to adjust some pair NonBondedForce interactions between the ligand and the...