Rules in Making the Transformation

One usage of the AlchemicalITP is to make the topology file for the transformation from one molecule (state A) to another molecule (state B). Certain rules are applied, when making this transformation.

Atomtypes

When the atomtype is given, AlchemicalITP will try to merge the Atomtypes from both topologies and remove the duplicate Atomtypes.

An additional atomtype dum will be added to represent dummy atom with no LJ.

[ Atomtypes ]
;  name at.num mass     charge ptype sigma epsilon
DUM     0      1.008000 0.0    A     0.0   0.0

Atoms

The atoms section will be treated differently based on the state of state B.

  • If the atom is the same in state B, the state B will be left blank.

  • If the mass, partial charge or atomtype is changed in state B, state B will be set up explicitly.

  • If the atom doesn’t exist in state A or state B, a dummy atomtype with no partial change and the same mass as the other state will be set up.

Bonded interactions

The bonds, pairs, angles and dihedrals are set up, such that:

  • if an interaction is the same in state A and state B, state B will be left blank.

  • If an interaction is present in both state A and state B, state B will be filled to reflect this change.

  • If any interactions involve dummy atoms, the parameter when all the atoms are present will be used.

cmap

If cmap is present, it can be read and write as it is but alchemical transformation involving the cmap is not supported.