Re: [AMBER] Size of solvent box, RDF

From: Krantzman, Kristin D <>
Date: Fri, 5 Feb 2016 17:44:27 +0000

Hi Carlos,
Thank you for responding.
I know this seems like a silly question, but how can I tell whether the protein interacts with its periodic images?
Best, Kristin

Sent from my iPad

> On Feb 5, 2016, at 7:10 AM, Carlos Simmerling <> wrote:
> 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" <> 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 []
>> 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 <>
>> wrote:
>>> On Wed, Feb 3, 2016 at 12:27 PM, Krantzman, Kristin D <
>>> 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?
>>> ‚ÄčThere'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
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Received on Fri Feb 05 2016 - 10:00:03 PST
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