I'd add to what Jason said that much depends on what you mean by "initial
solvent box". do you mean the actual size of the box, or the minimum
distance from solute atom to edge of the box? If the latter, what is the
conformation of the peptide when you created this box, and do you expect it
to vary? as the conformation changes, the compactness of the peptide may
change, also changing whether the box size is appropriate for that portion
of the simulation. It could be that you don't see artifacts during initial
tests, but during a much longer run with more conformational variability,
the evaluation from the initial test may no longer remain valid.
for simulations of a stably folded protein, this normally isn't a concern,
but since you said peptide I thought I'd mention it.
On Wed, Feb 3, 2016 at 1:31 PM, Jason Swails <jason.swails.gmail.com> wrote:
> On Wed, Feb 3, 2016 at 12:27 PM, Krantzman, Kristin D <KrantzmanK.cofc.edu
> >
> wrote:
>
> > Dear Amber Mailing List:
> > I am using AMBER to run md simulations of a 20 residue polypeptide in a
> > TIP3BOX explicit solvent.
> > I have performed simulations using an initial solvent box of 10.0
> > Angstroms and also with 15.0 Angstroms.
> > The non-bonded cutoff I have been using is 9.0 Angstroms.
> > What affects should I be observing if the solvent box is too small?
> >
>
> There's the obvious one that your simulation simply won't work. The
> minimum image convention is only valid if your cutoff is at least half the
> distance between the closest two planes of the triclinic unit cell being
> used for periodic boundary conditions. If this is not satisfied, then
> multiple periodic images of some atoms *may* be inside your cutoff. But
> most codes will catch this situation and quit with an error rather than run
> incorrectly (Amber included).
>
> The less obvious one is to check solvent radial distribution functions.
> The RDF densities should approach bulk solvent density asymptotically, and
> the initial peaks and valleys result from the ordered arrangement of
> solvent in the various solvation shells. Your box is too small if the
> solvent still feels the effect of the solute at the boundary of the unit
> cell, because that indicates a direct, solvent-mediated interaction between
> periodic images of the biomolecule.
>
> Basically what you are looking for is evidence of periodicity artifacts or
> evidence that periodic images of the solute are influencing each other.
> The RDF check is clear evidence that such an interaction exists, but is not
> (to my knowledge) sufficient that such interactions don't exist (if the
> RDFs *are* asymptotically "correct"). Other people may have other tidbits,
> though.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Wed Feb 03 2016 - 11:00:05 PST
