# special bonds

Hi users,

For better understanding of special bonds,

I constructed six member benzene ring ( no hydrogens) with atom id’s ( 1-2-3-4-5-6).

Without special bonds, van der Waals energy is Zero ( very much clear to me)

Now, I included special bonds 0.0 0.0 1.0 ( full scaling), Evdwl results in energy, say 'X’ kcal/mol.

Manually, I calculated energy for six pairs, ( 1-4, 2-5, 3-6, 4-1, 5-2, 6-3), this results in exactly double the energy 2X kcal/mol.

I understand this to be, special bonds pairs 1-4 resulting from dihedral 1-2-3-4 and 4-1 resulting from 4-5-6-1 are not allowed for duplication.

But actually, 1-4, 2-4, 3-6 has to be calculated twice right, since they are of different dihedrals.

spandana

Hi users,

For better understanding of special bonds,

I constructed six member benzene ring ( no hydrogens) with atom id's (
1-2-3-4-5-6).

Without special bonds, van der Waals energy is Zero ( very much clear to
me)

Now, I included special bonds 0.0 0.0 1.0 ( full scaling), Evdwl results
in energy, say 'X' kcal/mol.

Manually, I calculated energy for six pairs, ( 1-4, 2-5, 3-6, 4-1,
5-2, 6-3), this results in exactly double the energy 2X kcal/mol.

as it should. because you computed each pair twice.

I understand this to be, special bonds pairs 1-4 resulting from dihedral
1-2-3-4 and 4-1 resulting from 4-5-6-1 are not allowed for duplication.

But actually, 1-4, 2-4, 3-6 has to be calculated twice right, since they
are of different dihedrals.

no. 1-4 and 4-1 are the same pair and thus the pair interaction is
computed only once.

it doesn't matter how many times a pair shows up. once it is
identified as an 1-2, 1-3, or 1-4 pair (and 1-2 takes precedence over
and 1-3 as well as 1-3 over 1-4) the corresponding special_pair factor
determined whether the pair interaction is taken full, scaled or
excluded. that is it.

axel.