special_bonds command

Dear all

Hope you are fine.

To define an alkane molecule such as hexane I have defined its bonds, angles and cdihedrales according to amber forcefield. for non-bonded interactions I also have defined LJ and Columbic pair potentials.
I am wondering if we need to consider special bonds for alkanes such as n-hexane and n-decane?

Dear all

Hope you are fine.

To define an alkane molecule such as hexane I have defined its bonds, angles
and cdihedrales according to amber forcefield. for non-bonded interactions I
also have defined LJ and Columbic pair potentials.
I am wondering if we need to consider special bonds for alkanes such as
n-hexane and n-decane?

the choice of exclusions and possible scaling factors are part of the
force field. you need to refer to the corresponding publication(s).

axel.