>Note, "effective Born radius" has nothing to do with the surface area/nonpolar
calculation. It >is---qualitatively anyway---the average distance away from the
solvent (i.e., where the dielectric >constant switches from 1 to 80). It would
be worth familiarizing yourself with the general theory of >GB if this causes
confusion. The Amber manual offers a brief explanation with a number of
references >to look at for more detail.
Thank you for your suggestion.
I gave external dielectric constant value of 1, i.e., "extdiel = 1"
to also ignore electrostatic term in GB...
> Carlos
I'm sorry to forget show the column information with data.
resid1 ->resid2 |internal |vdw |eel |pol |sas
-----------------------------------------------------------------------
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
Sincerely yours,
-----Original Message-----
From: Carlos Simmerling [mailto:carlos.simmerling.gmail.com]
Sent: Wednesday, November 20, 2013 10:00 AM
To: AMBER Mailing List
Subject: Re: [AMBER] Res-Res energy shows different value with or without
explicit solvent
That's not correct. Gbsa=0 just turns off the surface area part.
I don't know what is in each column you quoted, so can't comment on that.
On Nov 19, 2013 7:45 PM, "kurisaki" <kurisaki.ncube.human.nagoya-u.ac.jp>
wrote:
>
> Both simulations were performed with the same input file shown below,
> But differ in presence or absence of explicit water molecules.
>
> > You have igb=1 set. This is continuum solvent.
> Yes, I use igb=1 because I found igb=0 does not work with idecomp in
> Amber12.
> But I set gbsa=0 to give zero value for GB-terms and in fact they are
> zero (see right two columns).
> Furthermore, internal, electrostatic, and vdW terms does not include
> GB terms, doesn't they?
>
> I do not think that GB affects such energy terms...
>
>
>
> -----Original Message-----
> From: Carlos Simmerling [mailto:carlos.simmerling.gmail.com]
> Sent: Tuesday, November 19, 2013 10:14 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] Res-Res energy shows different value with or
> without explicit solvent
>
> 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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> >
> >
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Received on Tue Nov 19 2013 - 18:30:02 PST
