Thank you for your reply, Prof. Roe,
> PS - By the way, what version of cpptraj are you using?
I use "CPPTRAJ: Trajectory Analysis. V14.05"
> I think that 1-4 electrostatics/van der Waals terms are included for
> idecomp energy decomposition 2 and 4; the 'pairwise' cpptraj command
> does not calculate these, so that may be where your differences are
> coming from (others who are more idecomp-savvy may want to correct me
> here). The total EEL/vdW energies I get from cpptraj match sander
> exactly.
I also checked idecomp 3 but the difference still remained.
I think 1-4 energy is cancelled when calculate inter-residue energy,
Namely, energy between two independent residues such like "235-> 298" in
mdout.
Best regards,
IK
> -----Original Message-----
> From: Daniel Roe [mailto:daniel.r.roe.gmail.com]
> Sent: Thursday, November 20, 2014 2:14 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] Pairwise vs Sander with imin=5
>
> Hi,
>
> I think that 1-4 electrostatics/van der Waals terms are included for
> idecomp energy decomposition 2 and 4; the 'pairwise' cpptraj command
> does not calculate these, so that may be where your differences are
> coming from (others who are more idecomp-savvy may want to correct me
> here). The total EEL/vdW energies I get from cpptraj match sander
> exactly.
>
> -Dan
>
> PS - By the way, what version of cpptraj are you using?
>
> On Wed, Nov 19, 2014 at 7:01 PM, kurisaki
> <kurisaki.ncube.human.nagoya-u.ac.jp> wrote:
> > Dear amber developers and uses,
> >
> > I'm now using "pairwise" in cpptraj to
> > Calculate inter-residue energy.
> >
> > Assuming residues A and B,
> > I calculated energy three times, i.e., for A, B and A+B.
> > Finally, I got inter-residue energy as Ene(A+B) - {Ene(A) + Ene(B)}.
> >
> > Now, I compaired the value with that obtained from sander with imin=5,
> and
> > idecomp = 4.
> > It is "almost" a half of the "pairwise" value.
> > I am assuming that "sander value" is divided by two
> > To assign inter-residue energy for each residue.
> >
> > Is this observation right?
> >
> > Even so, I found the difference between sander and pairwise by ca 1
> kcal/mol,
> > (for pairwise and sander, -96.6274 and -94.492 (2 x -47.246) [kcal/mol],
> > respectively)
> > Although I used the same value for non-bonded cutoff of value, 99 [A] for
> each
> > computation.
> >
> > Considering that each calculation is executed under the vacuum.
> > This inconsistensy seems strange.
> > Is there any additional difference between sander and pairwise?
> >
> > Thank you for your support.
> >
> > Best regards,
> >
> > Ikuo KURISAKI
> >
> > PS
> >
> > I believe "idecomp =3 or 4" does not make difference
> > When inter-residue energy is calculated.
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Wed Nov 19 2014 - 22:30:02 PST
