acemd.utils module#

acemd.utils.plumed_parser(fn)#
acemd.utils.view_forces(mol, forcefile, step=0, threshold=500, normalize=True, scalef=100)#

Visualize force vectors in VMD

Parameters:

  • mol (moleculekit.molecule.Molecule) – The Molecule with the coordinates on which to visualize the forces

  • forcefile (str) – The force file produced by ACEMD

  • step (int) – The simulation step for which to show the forces and coordinates

  • threshold (float) – Will only visualize forces with a magnitude above this threshold

  • normalize (bool) – If set to True it will normalize the force vectors to unit length

  • scalef (float) – Scaling factor by which to divide the force vectors (not used if normalize=True)