acemd.restraints module

class acemd.restraints.IntermolecularRepulsion(sel, sigma, epsilon, sel2=None)

Bases: object

Excluded-volume repulsion between distinct molecules of a selection.

Purely repulsive WCA among the selected atoms, with same-molecule pairs excluded, leaving their interaction with everything else untouched. Stops copies of a molecule aggregating: cosolvent probes, ligand copies, ions. sel2 repels two groups from each other instead; the intramolecular exclusion stays on so overlapping selections cannot repel one molecule apart.

sigma is deliberately far above any atomic LJ sigma, so each atom becomes a broad soft sphere so molecules repel as blobs. Coarse on purpose.

From the fragment-repulsion term in acerelax, itself following openmm/openmm#4853

ENERGY = '(1-delta(body1-body2))*step(rcut - r) * (4*epsilon*((sigma/r)^12 - (sigma/r)^6) + epsilon); rcut = 2^(1/6) * sigma; sigma=0.5*(sigma1+sigma2); epsilon = sqrt(epsilon1*epsilon2);'

WCA_CUTOFF_FACTOR = 1.122462048309373

static from_restraint_dict(restraint_dict)

static parse_restraint(restraint)

setupForce(idx, mol, fbrefmol, timestep, directory, system=None)

to_dict()

class acemd.restraints.PositionalRestraint(sel, axes='xyz', fb_width=None, fb_center=None, fb_center_offset=None, setpoints=None, legacy=False)

Bases: object

static from_restraint_dict(restraint_dict)

static from_restraint_str(restraint_str)

static parse_restraint(restraint)

setupForce(idx, mol, fbrefmol, timestep, directory, system=None)

to_dict()

acemd.restraints.get_force_str(axes, i, x1, x2, y1, y2, z1, z2, center_offset, distfun)

acemd.restraints.parse_setpoint(setpoint, timestep)

acemd.restraints.parse_setpoints(_setpoints, timestep)

acemd.restraints.setup_extforces(mol, restraints, fbrefcoor, system, timestep, directory)

acemd.restraints.update_restraints(simulation, restraints, step, log=False)