Wednesday, January 27, 2010

It's all about boundaries

Fig3-8
Figure 3.8. (a) Adenine (C5H5N5) in a liquid drop of 246 water molecules. (b) Adenine in a periodic box of 511 water molecules.
From Molecular Modeling Basics CRC Press, May 2010.

Conceptually, the simplest way of simulating a molecule in solution is to place it in the middle of a roughly spherical ball of water molecules (Figure 3.8a) and perform an molecular dynamics simulation.

One problem is this approach is that the drop would eventually evaporate if the simulation is run long enough. Another problem with the liquid drop model is that the water molecules at the surface of the drop do not behave like water molecules in liquid water.

Therefore, most explicit solvation simulations use periodic boundary conditions (Figure 3.9).

Fig3-9
Figure 3.9. Sketch of periodic boundary in two dimensions: (a) The position of the particles in the central box are copied and placed in neighboring boxes. Figure 3.8b shows a cube from a real simulation. (b) When a molecule tries to leave the box during an MD simulation, it reappears at the opposite end of the box, so the number of particles in the central box stays constant.
From Molecular Modeling Basics CRC Press, May 2010.

You can find interactive versions of Figures 3.8a and 3.9b here (I am grateful to Kestutis Aidas for providing the coordinates).

Click on the picture for an interactive version
Click on the picture for an interactive version

And you can find an animated version of Figure 3.9 here (an example of where a movie really is worth 10,000 words).


The animation was made with Molecular Workbench (MW). You can play with the simulation here or you can download the MW file here (after you gave installed MW).
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