Dear Dr, Case,
Thank you for your kind advise.
Best regards
2015-08-20 11:51 GMT-04:00 David A Case <david.case.rutgers.edu>:
> On Thu, Aug 20, 2015, Investigador Química wrote:
>
> > You are right. For the three isolated and solvated systems generated
> using
> > "solvateoct TIP3PBOX 11" we have:
> >
> > Box (x=y=z) triangulated 3-points waters sum of
> charges
> >
> > H-G 64,477 6598 -0.99950000
> > H 51,248 3254 -0.16460000
> > G 37,612 1321 -0.03280000
> >
> > My problem is how can I run the simulations with the water counts exactly
> > matched between the bound and unbound simulations?
>
> This is not likely to ever work in the way you want (if I understand what
> you are trying to do). The fluctuations in the water-water energies,
> and the box-size dependencies of the total energies, are likely to make
> any direct subtraction of explicitly solvated total energies extremely
> difficult to converge. This is *not* the way people in the macromolecular
> or host-guest fields go about estimating association energies.
>
> To see what is involved (and what you want to do is really quite
> difficult),
> look at these papers:
>
> %A J.C. Gumbart
> %A B. Roux
> %A C. Chipot
> %T Standard Binding Free Energies from Computer Simulations: What Is the
> Best
> Strategy?
> %J J. Chem. Theory Comput.
> %V 9
> %P 794-802
> %D 2012
>
> %A J.C. Gumbart
> %A B. Roux
> %A C. Chipot
> %T Efficient Determination of Protein-Protein Standard Binding Free
> Energies
> from First Principles
> %J J. Chem. Theory Comput.
> %V 9
> %P 3789-3798
> %D 2013
>
> [An aside: your values above for "sum of charges" look very odd: what is
> going
> on?]
>
> ...dac
>
>
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--
Área de Software
Investigación Facultad de Química
Universidad de Santiago de Chile
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Received on Sat Aug 22 2015 - 14:00:05 PDT
