# Re: [AMBER] Inconsistent Internal energy from monomer to dimer

From: Carlos Simmerling <carlos.simmerling.gmail.com>
Date: Wed, 4 Apr 2012 05:37:37 -0400

i'm not sure i understand your statements here, and I want to make sure its
clear.
you calculated 3 trajectory energies- the dimer trajectory (AB), and then
each of the 2 monomers from the same trajectory (A+B). You're saying that
A+B still isn't equal to AB. I'm asking because below you only quote 2
energies, and I'm not sure if you mean to say that the split monomers had
identical energies (possible, but seems unlikely).
If this is the case, then something is clearly wrong with the energy
calculations (or perhaps in the inputs).
Can you confirm, and provide all 3 energy values?

On Wed, Apr 4, 2012 at 3:40 AM, Josep Maria Campanera Alsina <
campaxic.gmail.com> wrote:

> Dear,
> I undertook also the test that Carlos suggests but the result was
> consistent with dimer energies. I splitted up the dimer into two
> monomer trajectories and later on I computed the MMGBSA for each of
> them. The result was an internal energy (BOND, ANGLES, DIHED) of
> approximately for each trajectory of 567 kcal/mol (1135.89/2) whereas
> the INT energy for the free monomer was computed 545 kcal/mol so a
> difference of 22 kcal/mol.
>
> In line of what Carlos says is the fact that the BOND term is
> consistent between monomer and dimer (it doubles its value) but the
> origin of the inconsistency are the ANGLES and DIHED terms. See the
> attached file. However how can it be a 22 kcal/mol difference in the
> internal energy between a free monomer and monomer with the
> constraints of a partner? I think something is wrong here.
>
> All comments will be welcome. Thanks Carlos.
>
> Josep Maria,
>
> > Message: 1
> > Date: Tue, 3 Apr 2012 07:25:32 -0400
> > From: Carlos Simmerling <carlos.simmerling.gmail.com>
> > Subject: Re: [AMBER] Inconsistent Internal energy from monomer to
> > dimer
> > To: AMBER Mailing List <amber.ambermd.org>
> > Message-ID:
> > <
> CAGk3s-Qp_8mk-87T3OKp4LSysgWj-2wWUbBs-qbZ02ATenvR8Q.mail.gmail.com>
> > Content-Type: text/plain; charset=ISO-8859-1
> >
> > in order to check the code, I think the right way to go is to use ptraj
> to
> > split the dimer trajectory into 2 monomer trajectories. then the
> > conformations are the same, so the energies should match. I can
> completely
> > expect that the dimer trajectory has different structure than the
> monomer,
> > and so the dihedral energies are different. perhaps the dimer optimizes
> > nonbonded interactions, and in the monomer the dihedrals can relax
> wityhout
> > the nonbonded constraints.
> >
> > On Tue, Apr 3, 2012 at 7:15 AM, Josep Maria Campanera Alsina <
> > campaxic.gmail.com> wrote:
> >
> >> Dear all,
> >>
> >> I have found an inconsistency in MMGBSA/PBSA calculations that
> >> embittering me. This is about the internal INT term (BOND+ ANGLES
> >> +DIHEDRALS) in the MMGSBA decomposition only. A colleague has passed
> >> to me two simulations run apparently under the same conditions in
> >> AMBER11. One simulation consists of a peptide of 26 residues (408
> >> atoms) and the other one a dimer of the SAME peptide with 52 residues
> >> (816 atoms), the double of the same atoms. I've run the MMGBSA
> >> analysis (AMBER11 perl and python scripts) and the INT term
> >> (BOND+ANGLE+DIHED) of the DIMER (1135.89 kcal/mol) is not, by far, the
> >> double of the INT term of the MONOMER (545.67 kcal/mol). I would just
> >> expect approximately a double value. Actually, there is a difference
> >> of 22 kcal/mol (1135.89/2-545.67)!!!!!!!!
> >>
> >> Here is my question, How can be that the internal energy per monomer
> >> unit changes so much? I think it cannot be! BOND, ANGLES AND DIHED
> >> cannot be so different in both systems, actually should be very
> >> similar in terms of monomer units. I've been trying a lot of things
> >> (topology files, amber inputs etc.) to correct this but I haven't
> >> found anything strange, neither in the dynamics nor in the MMGBSA!
> >> What do you think? Is this energy values normal? What's wrong here?
> >> Where should I focus?
> >>
> >> All comments will be welcome.
> >>
> >> Josep M.,
> >>
> >> PD: Find attached amber files for inspection.
> >>
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> >>
>
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Received on Wed Apr 04 2012 - 03:00:04 PDT
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