parmed.tools.coarsegrain module

This module handles adding coarse graining data to topology files set up by Luciana Capece. It has been implemented here in parmed by Jason Swails, but all ideas were Luciana’s. Here is a description of what this section does to topology files:

ANGLE_FORCE_CONSTANT has been rigged to provide an integer index to the specific parameter found in the given parameter file. This will be used to set up 4 different (new) prmtop sections: ANGLE_COEF_A, ANGLE_COEF_B, ANGLE_COEF_C, and ANGLE_COEF_D. ANGLE_FORCE_CONSTANT now becomes useless, so I will add a comment to the topology file saying such.

DIHEDRAL_FORCE_CONSTANT has been rigged in much the same way, creating 8 new sections: DIHEDRAL_AMPLITUDE_1,2,3,4 and DIHEDRAL_PHASE_1,2,3,4. DIHEDRAL_FORCE_CONSTANT, DIHEDRAL_PHASE, and DIHEDRAL_PERIODICITY become useless and are commented as such (though not removed).

This module sets up ANGLE and DIHEDRAL classes to make printing them easier, then parses the parameter file, then sets the respective sections of the prmtop file.

class parmed.tools.coarsegrain.Angle(atom1, atom2, atom3, acoef, bcoef, ccoef, dcoef)

Bases: object

Angle between 3 bonded atoms

class parmed.tools.coarsegrain.Dihedral(atom1, atom2, atom3, atom4, ampl1, ampl2, ampl3, ampl4, phase1, phase2, phase3, phase4)

Bases: object

Dihedral between 4 bonded atoms

parmed.tools.coarsegrain.addCoarseGrain(parm, param_file)