Re: Questions on periodic boundary condition

From: LEWYN LI (
Date: Thu Sep 02 2004 - 11:00:47 CDT

Dear Ed,

         Thank you very much! Your explanation is very clear and helpful.


On Thu, 2 Sep 2004, Edward Patrick Obrien wrote:

> On Thu, 2 Sep 2004, LEWYN LI wrote:
>> I just have two questions that I hope someone could help me with:
>> 1. I am pulling a protein in SMD, and I see that some of the sidechains are
>> moving out of the water box during the simulation movie. Since I was using
>> periodic boundary condition, I am confused if these sidechains are truly out of
>> the box, or are the sidechains still solvated by (invisible) image water
>> molecules?
> If you have invoked PBC's then yes your sidechains are out of your defined
> Periodic box, and yes the sidechains are still solvated by water
> molecules in another portion of the Periodic box. It is fine if any atoms
> move outside the defined periodic box.
>> 2. Our protein is pretty big, and there are only 1 - 2 water layers above and
>> below the protein after equilibration. With periodic boundary condition, I
>> understand that this would mean there will be only 2 - 4 water layers between
>> the protein and its image in another cell. Is my understanding correct? And
>> what kind of artifacts may this introduce into the simulation?
>> Thank you very much for your help!
> If you look at the radial distribution function of water (Oxygen-Oxygen)
> you will see a correlation up to 3 water molecules in length (~9
> angstroms), after which distance bulk density is reached and there is no
> more correlation.
> Because of this correlation of water molecules, I believe it is good
> practice to make sure that the minimum number of water molecules between
> the protein and the Periodic boundary is 3, or in other words there should
> be atleast 6 water molecules between the protein and its' image.
> If you don't have this situation then water may not display its proper
> bulk behavior, which could mean your solvation shell around the protein is
> being influenced by the the image protein.
> That is the only artifact I can think of.
> Due to the computational cost of having three layers of water at all
> times many researchers publish results with less then this.
> I don't know of a systematic study of water layer / PBC artifacts,
> although I'm sure somebody has.
> Hope that helps,
> Ed

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