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.