You'll probably want to make sure the unfolding is reproducible for the box
size, otherwise your 2 observations could just be variability in unfolding
time across runs and not related to box.
Does the protein interact with periodic images when it unfolds?
On Feb 4, 2016 1:43 PM, "Krantzman, Kristin D" <KrantzmanK.cofc.edu> wrote:
> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> >
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Received on Fri Feb 05 2016 - 04:30:03 PST
