¶ Xponge.forcefield.special.fep
This module gives the basic functions for fep calculations
¶ subpackages
¶ submodules
¶ functions
¶ save_hard_core_lj
This function is used to save hard core lj
¶ save_soft_core_lj
This function is used to save soft core lj
¶ write_soft_lj
| parameters |
explanation |
| self |
|
¶ intramolecule_nb_to_nb14
This function convert the non bonded interactions to nb14 interactions within the molecule
| parameters |
explanation |
| mol_a |
the Molecule instance |
| perturbating_residues |
the residue(s) to be perturbed |
¶ get_free_molecule
This function makes the molecule to be "free", having no interaction with other molecules
| parameters |
explanation |
| mol_a |
the Molecule instance |
| perturbating_residues |
the residues to be perturbed |
| intra_fep |
whether clear intramolecular non bonded interactions |
| return |
a new Molecule instance |
¶ merge_force_field
This function merges one molecule in two different force fields (two Molecule instances) into one
| parameters |
explanation |
| mol_a |
the Molecule instance in the initial lambda stat |
| mol_b |
the Molecule instance in the final lambda stat |
| default_lambda |
the lambda to scale the force if no specific_lambda is set for the force |
| specific_lambda |
a dict to map the force to its special scale factor lambda |
| intra_fep |
whether clear intramolecular non bonded interactions |
| return |
the Molecule instance merged |
