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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Received on Fri Aug 14 2015 - 11:30:03 PDT
