You have igb=1 set. This is continuum solvent. You only give 1 input file
so I don't know which calculations you are comparing. Including continuum
solvent along with explicit solvent will certainly give a different result
from continuum solvent and no explicit solvent. The effective Born radii
for the atoms will differ, thus the solvation energy will differ.
On Nov 19, 2013 8:06 AM, "kurisaki" <kurisaki.ncube.human.nagoya-u.ac.jp>
wrote:
> Thank you for your answer, Jason.
>
> I'm so sorry to miss to tell you my simulation condition.
> I perform both simulations in free-boundary condition.
>
> The input file is here:
>
> #decompose energy on a residue pair basis on the trajectory
> &cntrl
> imin = 5, igb = 1, gbsa = 0, rgbmax = 8.21,
> ntx = 1, maxcyc = 1,
> ntc = 2, ntf = 2,
> ntb = 0, ntp = 0,
> ntwe = 0, ntpr = 1, ntwx=1,
> cut = 99, idecomp = 3,
> extdiel = 1,
> /
> Residues considered as REC
> RRES 1 295
> END
> Residues considered as LIG
> LRES 296 296
> END
> Residues to print
> RES 79 79 135 135 241 241
> END
> END
>
> As shown above, periodic boundary condition is set to off by ntb=0.
> Furthermore, each snapshot was not energetically minimized.
>
> So, I find the difference between them is derived from
> Alternative reason but ewald term...
>
> Ikuo KURISAKI
>
>
>
>
>
>
> -----Original Message-----
> From: Jason Swails [mailto:jason.swails.gmail.com]
> Sent: Tuesday, November 19, 2013 9:54 PM
> To: amber.ambermd.org
> Subject: Re: [AMBER] Res-Res energy shows different value with or without
> explicit solvent
>
> On Tue, 2013-11-19 at 21:06 +0900, kurisaki wrote:
> > Dear Amber Users,
> >
> > I found that Res-Res energy shows different value
> > With or without explicit solvent, i.e.,
> >
> > With solvent
> > TDC 79-> 79 0.000 -1.567 -5.462 0.000 0.000
> >
> > Without solvent
> > TDC 79-> 79 0.000 -1.346 -5.709 0.000 0.000
> >
> >
> > I thought that res-res energy meant direct non-bonded interaction energy
> > between the two residues, but does it include energetic contribution from
> > the other all residues?
>
> The direct-space electrostatic term in PME is screened. The
> electrostatic term in implicit solvent is not. The direct-space
> screening in PME is removed in the reciprocal space part of the PME
> calculation, and this part is _not_ decomposable. As a result, I think
> it is likely ignored.
>
> The screening (which is caused by an artificial neutralizing charge
> distribution centered on each particle) is part of the Ewald technique
> for computing electrostatic energies in an infinitely periodic system.
> The Allen and Tildesley book has a nice description of it (as do several
> other general computational chemistry books).
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
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Received on Tue Nov 19 2013 - 05:30:03 PST
