Dear Jason, thank you for your kind explanation. I recognize my first
question was not fortunate. Please let me to explain my question.
If I have the Etot for a host H, for a guest G and for the complex H-G, I
can calculate the interaction energy as E= E(complex H-G) - E(H) - E(G),
isn't?. If I get the energies for the three entities using solvateoct and
TIP3PBOX from 8 to 11 each time (for the three entities each time) I get
different interaction energies. Should the interaction energy best value be
the lower one? How can I know that, if I have no experimental values to
compare with? For instance these were the values I got when running 3 ns
of MD equilibration according to AMBER tutorial 1 section 5:
box 8: E= -11067 kcal/mol
box 9: E= -10363 kcal/mol
box 10: E= -8276 kcal/mol
box 11: E= -6485 kcal/mol
(H has 480 atoms. G has 68 atoms)
Thank you for your help
2015-08-14 14:12 GMT-04:00 Jason Swails <jason.swails.gmail.com>:
> On Fri, Aug 14, 2015 at 1:45 PM, Investigador Química <
> investigacion.faq.gmail.com> wrote:
>
> > Dear Sirs:
> >
> > Could you please help me to set up the better box size for AMBER
> > calculation.
> >
>
> Define "better".
>
>
> > We have used solvateoct with 8.0 , 9.0 , 10.0 and 11.0. And we get
> > different Etot values.
> >
>
> Of course you do. Energy is an extensive property, so it depends on the
> number of particles in your simulation.
>
> There are offsetting costs between smaller and larger solvent boxes.
> Smaller boxes are more likely to yield artifacts due to periodic images of
> the solute interacting with each other (and other effects associated with
> the much higher effective concentrations). Larger boxes have more atoms
> (obviously), and so you can't sample as much as you can with a smaller
> box. Somewhere between 10 and 15 Angstroms is typically a fine choice,
> although it's not appropriate for all applications.
>
> The bigger your box, the "better" your simulation, since it reduces
> periodicity artifacts. The smaller your box, the "better" your sampling,
> since it has fewer atoms. "best" is some undetermined compromise between
> the two.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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> AMBER.ambermd.org
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>
--
Área de Software
Investigación Facultad de Química
Universidad de Santiago de Chile
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Received on Wed Aug 19 2015 - 08:00:03 PDT
