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Dofulator

This library provides a degrees of freedom (DoF) calculator for molecular dynamics simulations which use rigid geometry constraints. Per-atom and per-direction DoF are calculated using the methods described in J. Chem. Theory Comput. 2024, 20, 23, 10615–10624, which are applicable to both rigid bodies and semi-rigid fragments.

The core library is provided as a C API (see the usage docs or dofulator.h). A Python wrapper is also provided, and includes some plugins compatible with MDAnalysis (some example usage is shown below).

For further details, see the documentation.

Installation

See here for full installation details.

To quickly set up for usage with MDAnalysis:

pip install "dofulator[mdanalysis]@git+https://github.com/CTCMS-UQ/dofulator.git"

MDAnalysis examples

Directional DoF of all atoms

import MDAnalysis as mda
from dofulator import MDADofulator
u = mda.Universe('topology.tpr', 'trajectory.trr')
d = MDADofulator(
    u.atoms,            # Include all relevant atoms in the dofulator context
    rigid_bonds=[b for b in u.bonds if b.type == '3'],          # Set bond type 3 as rigid
    rigid_bodies=[r for r in u.residues if r.resname == 'H2O'], # Water treated as rigid bodies
    mode='directional'  # Options are 'atomic' (default) or 'directional'
)
d.run()
# Access results via d.results

Temperature profile across system

For local temperature calculation, the LocalTemperature class makes use of MDAnalysis' AtomGroups, which can dynamically update as the trajectory plays.

import MDAnalysis as mda
import numpy as np
from dofulator import MDADofulator, LocalTemperature
u = mda.Universe('topology.tpr', 'trajectory.trr')
zrange = np.linspace(0, u.dimensions[2], 11) # 10 bins in the z direction
t = LocalTemperature(
    # List of atom selections, each of which will get temperature calculated on each frame
    [u.select_atoms(f'prop z >= {zrange[i]} and prop z < {zrange[i+1]}', updating=True)
        for i in range(len(zrange) - 1)],

    # Dofulator context for calculating DoF in each selection
    MDADofulator(
        u.atoms,            # Include all atoms which could be selected
        rigid_bonds=[b for b in u.bonds if b[0].type == 'H' or b[1].type == 'H'], # Rigid bonds to hydrogens
    )
)
t.run()
# t.results contains an n_frames x 10 array with temperature of each bin on each frame

Citation

When using dofulator in published work, please cite the following paper:

  1. S. Sanderson, S. R. Tee, and D. J. Searles; Local Temperature Measurement in Molecular Dynamics Simulations with Rigid Constraints Journal of Chemical Theory and Computation 2024 20 (23), 10615–10624. DOI: 10.1021/acs.jctc.4c00957