Confusion in [ dihedrals ] section in hybrid topology

[wagleswapnil]

Hi, I generated a hybrid topology of two ligands, the [ dihedrals ] section of the hybrid topology looks like this:
[ dihedrals ]
; ai aj ak al funct c0 c1 c2 c3 c4 c5
1 10 9 3 1 180 15.3215155 2 180 0 2 ; C1x C10x C9x C3x (AAAA->DDDD)
1 10 9 3 1 180 0 2 180 15.3215155 2 ; C1x C10x C9x C3x (AAAA->DDDD)
1 10 9 8 1 180 15.3215155 2 180 0 2 ; C1x C10x C9x C8x (AAAA->DDDD)
1 10 9 8 1 180 0 2 180 15.3215155 2 ; C1x C10x C9x C8x (AAAA->DDDD)
1 11 2 3 1 180 24.7411728 2 180 0 2 ; C1x N1x C2x C3x (AAAA->DDDD)
1 11 2 3 1 180 0 2 180 24.7411728 2 ; C1x N1x C2x C3x (AAAA->DDDD)
1 11 2 23 1 180 15.6141438 2 180 0 2 ; C1x N1x C2x H2x (AAAA->DDDD)
1 11 2 23 1 180 0 2 180 15.6141438 2 ; C1x N1x C2x H2x (AAAA->DDDD)
2 3 4 12 1 180 4.8669776 2 180 0 2 ; C2x C3x C4x C11x (AAAA->DDAA)
2 3 4 12 1 180 0 2 180 0.48669776 2 ; C2x C3x C4x C11x (AAAA->DDAA)
....

The dihedrals for almost all the pairs are defined twice. So, I have 2 questions about this [ dihedrals ] output:

1. I want to simulate just the end states A and B in equilibrium runs. Are all the force constants for dihedrals for state A turned to 0, as the latest entries for the dihedrals will be considered?
2. If I want to write ifdef LIGAND_A and ifdef LIGAND_B sections for the dihedrals, which contain the dihedrals for ligand A and ligand B on both the left and right sides in the entries, respectively, should it look like this? :
   [ dihedrals ]
   #ifdef LIGAND_A
   1 10 9 3 1 180 15.3215155 2 180 15.3215155 2 ; C1x C10x C9x C3x (AAAA->DDDD)
   1 10 9 3 1 180 0 2 180 0 2 ; C1x C10x C9x C3x (AAAA->DDDD)
   1 10 9 8 1 180 15.3215155 2 180 15.3215155 2 ; C1x C10x C9x C8x (AAAA->DDDD)
   1 10 9 8 1 180 0 2 180 0 2 ; C1x C10x C9x C8x (AAAA->DDDD)
   1 11 2 3 1 180 24.7411728 2 180 24.7411728 2 ; C1x N1x C2x C3x (AAAA->DDDD)
   1 11 2 3 1 180 0 2 180 0 2 ; C1x N1x C2x C3x (AAAA->DDDD)
   ....
   #endif
   #ifdef LIGAND_B
   1 10 9 3 1 180 0 2 180 0 2 ; C1x C10x C9x C3x (AAAA->DDDD)
   1 10 9 3 1 180 15.3215155 2 180 15.3215155 2 ; C1x C10x C9x C3x (AAAA->DDDD)
   1 10 9 8 1 180 0 2 180 0 2 ; C1x C10x C9x C8x (AAAA->DDDD)
   1 10 9 8 1 180 15.3215155 2 180 15.3215155 2 ; C1x C10x C9x C8x (AAAA->DDDD)
   1 11 2 3 1 180 0 2 180 0 2 ; C1x N1x C2x C3x (AAAA->DDDD)
   1 11 2 3 1 180 24.7411728 2 180 24.7411728 2 ; C1x N1x C2x C3x (AAAA->DDDD)
   1 11 2 23 1 180 0 2 180 0 2 ; C1x N1x C2x H2x (AAAA->DDDD)
   1 11 2 23 1 180 15.6141438 2 180 15.6141438 2 ; C1x N1x C2x H2x (AAAA->DDDD)
   ....
   #endif
   #ifdef LIGAND_AB
   1 10 9 3 1 180 15.3215155 2 180 0 2 ; C1x C10x C9x C3x (AAAA->DDDD)
   1 10 9 3 1 180 0 2 180 15.3215155 2 ; C1x C10x C9x C3x (AAAA->DDDD)
   1 10 9 8 1 180 15.3215155 2 180 0 2 ; C1x C10x C9x C8x (AAAA->DDDD)
   1 10 9 8 1 180 0 2 180 15.3215155 2 ; C1x C10x C9x C8x (AAAA->DDDD)
   1 11 2 3 1 180 24.7411728 2 180 0 2 ; C1x N1x C2x C3x (AAAA->DDDD)
   1 11 2 3 1 180 0 2 180 24.7411728 2 ; C1x N1x C2x C3x (AAAA->DDDD)
   1 11 2 23 1 180 15.6141438 2 180 0 2 ; C1x N1x C2x H2x (AAAA->DDDD)
   1 11 2 23 1 180 0 2 180 15.6141438 2 ; C1x N1x C2x H2x (AAAA->DDDD)
   2 3 4 12 1 180 4.8669776 2 180 0 2 ; C2x C3x C4x C11x (AAAA->DDAA)
   2 3 4 12 1 180 0 2 180 0.48669776 2 ; C2x C3x C4x C11x (AAAA->DDAA)
   2 3 4 18 1 180 4.8669776 2 180 0 2 ; C2x C3x C4x C14x (AAAA->DDAA)
   2 3 4 18 1 180 0 2 180 0.48669776 2 ; C2x C3x C4x C14x (AAAA->DDAA)
   ...
   #endif

[vgapsys]

1. In a hybrid topology dihedral for ligand A is turned of, dihedral for ligand B is turned on. This topology can be used for equilibrium simulations in the states A and B, as well as for the transitions between the states
2. The ifdef definitions are not required: you can simply use hybrid topology as created by pmx and control which state is activated via mdp parameters

[nonsensejoke]

I'm also struggling to understand this section about dihedral.

Is there some detailed manual related to this? Or could you please point me to certain block of pmx code?

Thanks a lot.

[vgapsys]

The dihedrals are constructed here:

pmx/src/pmx/ligand_alchemy.py

Line 2509 in e6d6258

def _make_dihedrals( self ):