> When I looked at my output I found that I had 1-4 EEL = -149.6471. I don't
> quite understand why this value is anything but zero. I only have one type
> of dihedral in this system HO-x-x-x and for HO all of the atoms in the
> molecule are in it's excluded list, meaning that there should be no 1-4
> interactions according to my understanding. Is the energy for my
> electrostatic interactions only the value from EELEC or is it a combination
> of EELEC and 1-4 EEL?
The 1-4 interactions are calculated along with the dihedrals and
calculated once for each 1-4 interaction. Effectively, if you have your
system:
1-2-3-4
1 and 4 still have charges and van der Waals and their interactions need
to be calculated. As they are close in space, and have intervening
bonds/angles, in the past force approach sometimes these interactions are
screened. We do this with SCEE or SCNB in older AMBER, and now directly
in the prmtop. GLYCAM doesn't scale 1-4 electrostatics whereas ff9X
scales by 1.2.
So, yes, also 1 and 4 are excluded in the pairlist, the interaction is
still included however it is calculated as the dihedrals are evaluated.
In other words, the rotational profile for the bond 2-3 depends not only
on the dihedral potential but also the 1 + 4 charges and van der Waals
(and their potential scaling).
--tec3
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Received on Wed Apr 25 2012 - 12:00:04 PDT
