molecular_simulations.data.constant_ph_reference_energies module

Reference energies for constant pH simulations.

These reference energies are calibrated to give the correct pKa values for titratable residues. The convention is:

ref_energies[residue_type] = [E_deprotonated, E_protonated, …]

Where E_deprotonated = 0 and E_protonated = kT * ln(10) * pKa

This ensures that at pH = pKa, both protonation states have equal probability.

molecular_simulations.data.constant_ph_reference_energies.get_ref_energies(ff='amber19')

Get reference energies for constant pH simulations.

Parameters:

ff (str) – Force field name (currently only ‘amber19’ is supported)

Returns:

Maps residue type names to lists of reference energies (kJ/mol). Index 0 is the deprotonated state, index 1+ are protonated states.

Return type:

dict