From: Edward Patrick Obrien (edobrien_at_Glue.umd.edu)
Date: Thu Sep 02 2004 - 10:51:56 CDT
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
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
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,
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