On Thu, Jul 19, 2012 at 10:02 PM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> You could decompose the energies with no periodicity even if originally run
> with pme- the key thing really is whether you want just the coulomb
> energy, or some estimate of solvent contributions.
>
So like eedmeth=4 or 5? Would that still use the minimum image convention
and recognize periodicity? Or you would you potentially have to do some
funky imaging?
> On Jul 19, 2012 9:57 PM, "Jason Swails" <jason.swails.gmail.com> wrote:
>
> > As Carlos mentioned, you should try the "idecomp" flag to get what you
> > want. The problem with decomposing into pairwise interactions within a
> > system is that no potential energy functions that Amber uses are truly
> > pairwise decomposable for the electrostatic contributions.
> >
> > In implicit solvent, the dielectric boundary is defined by every atom in
> > the system, and since the solvation term depends on the definition of
> this
> > boundary (to distinguish between a 'buried' and 'exposed' residue),
> > interactions between 'pairs' of atoms or residues in this context will
> > include contributions from all other atoms in the system via the
> > calculation of the effective Born radii (GB) or the dielectric switching
> > function (PB). Furthermore, by using an implicit solvent model, you're
> > including the screening effects of the solvent molecules surrounding your
> > protein in your pairwise interaction.
> >
> > This type of decomposition is available through MMPBSA.py on a single
> > structure via a 'stability' calculation. If you want to know how two
> > protein residues interact, this is the route I suggest. ante-MMPBSA.py
> > will set up stripped topology files for you to run MMPBSA.py with.
> >
> > Explicit solvent (PME) carries with it a completely different set of
> > limitations. In Ewald sums, the electrostatic interaction is divided
> into
> > a short-range term and a long-range term (the first summed via a direct
> > sum-over-nearby-pairs and the latter summed in reciprocal space using a
> > FFT). The reciprocal space term in general is not pairwise decomposable
> > (I've been told you can play tricks, but it's not straightforward nor is
> it
> > implemented in Amber), and the direct-space sum is meaningless without it
> > (since it is artificially dampened with a neutralizing gaussian
> counterion
> > to reduce the required cutoff, and the effect of this artificial
> counterion
> > is reversed in the reciprocal space part). A quick glance at the code
> > suggests there is no decomposition accumulation in the reciprocal space
> > part, so I'm not even sure how you would interpret decomposed energies in
> > explicit solvent...
> >
> > Perhaps someone can clear up that last point for me if there is a
> > meaningful interpretation. In any case, I assert (perhaps incorrectly)
> > that pairwise-decomposed energies can be qualitatively helpful, but
> should
> > be taken with a grain of salt.
> >
> > HTH,
> > Jason
> >
> > On Thu, Jul 19, 2012 at 6:21 PM, Irene Newhouse <einew.hotmail.com>
> wrote:
> >
> > >
> > > I'm EXTREMELY interested in being able to do this myself! Someone
> please
> > > tell! Irene Newhouse
> > > > Date: Thu, 19 Jul 2012 18:47:25 -0300
> > > > From: bracht.iq.ufrj.br
> > > > To: amber.ambermd.org
> > > > Subject: [AMBER] Interaction energy between residue pairs
> > > >
> > > > Hello. If one had a molecular dynamics simulation of a solvated
> > > > protein (in this case, water is the solvent), and was interested in
> > > > retrieving VdW and Coulomb interaction energies between pairs of
> > > > residues (very specific pairs of residues. Just in case you are
> > > > wondering, there are no ligands, just protein residues) for this
> > > > particular simulation. What would be the best way to do this in
> Amber?
> > > > The idea here is see the effect that a mutated residue has in one(or
> > > > more) of the catalytic site residues.
> > > > Thank you
> > > > Fabrício Bracht
> > > >
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> >
> >
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Candidate
> > 352-392-4032
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Jul 19 2012 - 20:00:03 PDT
