Re: [AMBER] Size of solvent box, RDF

From: Krantzman, Kristin D <KrantzmanK.cofc.edu>
Date: Thu, 4 Feb 2016 18:42:50 +0000

Dear Jason and Carlos,
Thank you for answering me questions.
I meant the minimum distance from the solute atom to the edge of the box. The cutoff is less than half of the distance of the box length.

In the simulations with the smaller box, the protein loses its a-helix character after 8 ns. In the simulations with the larger box, the protein retains its a-helix character. I think that the polypeptide should retain its initial conformation.

Jason, I am not completely certain about the use of the radial command to calculate the RDF. My polypeptide consists of alanine residues.
Are these the correct commands?

radial radO.dat 0.1 10.0 :WAT.O :ALA
radial radH1.dat 0.1 10.0 :WAT.H1 :ALA
radial radH2.dat 0.1 10.0 :WAT.H2 :ALA

When I compare the RDF values calculated this way with the two different sizes of boxes, the curves look almost identical. The rdf value approaches 0.9 at the end of the solvent box for all cases. Is this what you mean by checking the bulk density?
Thanks in advance.
Best, Kristin
________________________________________
From: Carlos Simmerling [carlos.simmerling.gmail.com]
Sent: Wednesday, February 03, 2016 1:38 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Size of solvent box

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 Thu Feb 04 2016 - 11:00:03 PST
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