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
