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Nutmeg Potentials

This repository contains the Nutmeg machine learning potentials described in

Peter Eastman, Benjamin P. Pritchard, John D. Chodera, Thomas E. Markland. "Nutmeg and SPICE: Models and Data for Biomolecular Machine Learning." https://arxiv.org/abs/2406.13112

They are made available in several formats.

  1. Pytorch models in TorchScript format
  2. A potential function for use with OpenMM-ML
  3. A Calculator for use with ASE
  4. The source code and checkpoints for the original PhysicsML models

Instructions for using the first three are given below. The PhysicsML models are a less convenient form, and there is usually no reason to use them directly. They can be found in the source directory. They are not installed with the package.

Installation

  1. Download this repository.
  2. In a terminal, cd to the top level directory containing setup.py.
  3. Enter the command
pip install .

Usage: TorchScript models

The Pytorch models in TorchScript format are in the directory nutmegpotentials/models. You can load them with torch.jit.load().

import torch
model = torch.jit.load('nutmeg-small.pt')

Each model requires the following information as inputs.

  • The atomic positions in nm.
  • The elements of the atoms.
  • The Gasteiger partial charges of the atoms, as computed with RDKit. Other types of partial charges will probably not produce accurate results and should not be used.
  • The periodic box vectors in nm, if periodic boundary conditions are to be applied.

The following example uses RDKit to construct an alanine molecule from a SMILES string and compute the necessary information.

from rdkit import Chem
from rdkit.Chem import rdPartialCharges, rdDistGeom
mol = Chem.MolFromSmiles('C[CH](N)C(O)=O')
mol = Chem.AddHs(mol)
rdPartialCharges.ComputeGasteigerCharges(mol)
rdDistGeom.EmbedMultipleConfs(mol, numConfs=1)
positions = 0.1*mol.GetConformer(0).GetPositions()
symbols = [atom.GetSymbol() for atom in mol.GetAtoms()]
charges = [a.GetDoubleProp('_GasteigerCharge') for a in mol.GetAtoms()]

The elements and charges need to be passed to the model in a particular pre-digested form. You can use the create_atom_features() function to create the necessary input tensors. The positions and box vectors (if present) must also be passed as Pytorch tensors.

from nutmegpotentials import create_atom_features
types, node_attrs = create_atom_features(symbols, charges)
positions = torch.tensor(positions, dtype=torch.float32)

You can now invoke the model.

energy = model(positions, types, node_attrs, None)

The return value is the energy in kJ/mol. We have passed None for the box vectors so that periodic boundary conditions will not be applied. Alternatively we could pass a (3, 3) tensor with the vectors defining the periodic box.

Usage: OpenMM

This package includes a potential function for use with OpenMM-ML. Simply specify the name of the model to use.

import nutmegpotentials
from openmmml import MLPotential
potential = MLPotential('nutmeg-small')

You can then pass a Topology object to it from which to create a System. In addition, it needs Gasteiger partial charges for the atoms. One option is to pass an array of charges to createSystem().

system = potential.createSystem(topology, charges=charges)

As an alternative, it can use RDKit to automatically determine the partial charges. In that case you only need to provide the total charge of the system as an integer.

system = potential.createSystem(topology, total_charge=0)

You can also create mixed systems in which part is modelled with a Nutmeg model and part with a conventional force field. See the OpenMM-ML documentation for details.

Usage: ASE

This package includes a Calculator for use with ASE. To create it, you specify the name of the model to use, the Atoms object it will be used to simulate, the Gasteiger partial charges of the atoms, and the Pytorch device to perform computations on. The Atoms object must include atomic symbols.

import ase
import torch
from nutmegpotentials.nutmegcalculator import NutmegCalculator
atoms = ase.Atoms(symbols=symbols, positions=positions)
device = torch.device('cuda')
atoms.calc = NutmegCalculator('nutmeg-small', atoms, charges, device)

When setting positions for the Atoms object, remember that ASE measures distances in Angstroms. The Calculator automatically performs conversions between the units used by ASE and the ones used internally by the models.