Constant potential tutorial #49
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peastman
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Nov 2, 2025
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This is a well written tutorial. I wonder if it could be made simpler, though. Building everything by hand is complicated. What about this?
- Load a PDB file with the model.
- Use a ForceField to create a System. You can use a standard force field for the water and ions, and provide a minimal XML file for the AU residues.
- Provide code to take a System and "constant potentialify" it: add a ConstantPotentialForce, copy the Coulomb parameters from the NonbondedForce, set them to zero in the NonbondedForce.
This should take less code overall, and users will be able to copy it directly for their own simulations, even if they involve different molecules.
| " system.addConstraint(i_o, i_h2, L_OH)\n", | ||
| " system.addConstraint(i_h1, i_h2, L_HH)\n", | ||
| "\n", | ||
| " residue = topology.addResidue(\"WAT\", chain_water)\n", |
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| " # Get all of the charges, and find the sum of the electrode charges.\n", | ||
| " # We divide out OpenMM's units before passing charges to Python's sum() function.\n", | ||
| " charges = self._conp.getCharges(simulation.context).value_in_unit(openmm.unit.elementary_charge)\n", | ||
| " charge_i = sum([charges[i] for i in self._i_indices]) * openmm.unit.elementary_charge\n", | ||
| " charge_j = sum([charges[j] for j in self._j_indices]) * openmm.unit.elementary_charge\n", |
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You can use openmm.unit.sum(), which knows how to add Quantities.
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Adds a tutorial on setting up a constant potential simulation. Effectively shows how to replicate one data point from this paper.