So if I interpret this correctly, despite the fact that 1 and 4 are in the
excluded pair list, their interaction is not actually excluded in Amber's
calculations. Ok. Then my final question is how to interpret the energies
listed in the output file. For example if I had
NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 299.77 PRESS =
0.0
Etot = 707.7731 EKtot = 641.5643 EPtot =
66.2087
BOND = 72.1704 ANGLE = 267.0562 DIHED =
-67.7222
1-4 NB = 230.9346 1-4 EEL = -1262.2843 VDWAALS =
-107.9538
EELEC = 934.0078 EHBOND = 0.0000 RESTRAINT =
0.0000
>From this information if I wanted to say
"The electrostatic contribution to the potential energy is..."
should I choose =EELEC or =EELEC + 1-4 EEL
Similarly for the vdw (VDWAALS or VDWAALS + 1-4 NB) and dihedrals (DIHED or
DIHED + 1-4 NB + 1-4 EEL).
The overall question is have the 1-4 potentials listed already been added
to the results printed for eelec/vdw/dihed? If this is true listing the
1-4 potentials independently is just to give extra information but they
have already been taken into account for the other potentials.
Thanks so much! This is a really big help.
Camille
On Wed, Apr 25, 2012 at 11:34 AM, Thomas Cheatham <tec3.utah.edu> wrote:
>
> > 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 - 15:30:02 PDT
