5.2.3. gromacs.scaling – Partial tempering

Author:

Jan Domanski, @jandom

Added in version 0.5.0.

Helper functions for scaling gromacs topologies; useful for setting up simulations with Hamiltonian replicate exchange and partial tempering (REST2).

gromacs.scaling.scale_dihedrals(mol, dihedrals, scale, banned_lines=None)

Scale dihedral angles

gromacs.scaling.scale_impropers(mol, impropers, scale, banned_lines=None)

Scale improper dihedrals

gromacs.scaling.partial_tempering(topfile='processed.top', outfile='scaled.top', banned_lines='', scale_lipids=1.0, scale_protein=1.0)

Set up topology for partial tempering (REST2) replica exchange.

Changed in version 0.7.0: Use keyword arguments instead of an args Namespace object.