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.

Can anyone please help me to understand this.

Thanks in advance

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.