Water Simulation
for the Atlas of Macromolecules in Protein Explorer
Copyright © by Eric Martz, September 2004.
Permission is given to use this resource, or portions thereof, in websites or presentations provided the source, proteinexplorer.org, is cited.

Animated multi-GIF of water simulation. Unlike the displays in Chime, you cannot rotate the above molecules using the mouse.
Ten water molecules are initially arranged arbitrarily in two rows of five, not quite contacting each other. Their mutual chemical attractions then pull them into a compact micro-droplet. Each H2O molecule reorients itself to optimize the intermolecular interactions.

Both van der Waals and electrostatic energies were used in the energy minimization that produced this simulation, performed by the MDL Sculpt software package. The final conformation represents optimal hydrogen bonding for the small number of molecules involved. This simulation lacks the random motions that result from thermal energy. See further information about the methods below.

Challenge questions for students are below.

Troubleshooting: If the links below don't display something that looks like the small movie at right, please try starting Protein Explorer -- during start up, it automatically tests your browser and advises you how to configure it to work with the morphs below.

Challenge Questions for Students
Answering these questions by inspecting the simulation requires that it be viewed in MDL Chime or Protein Explorer.

  1. In the final (compact droplet) conformation, what is the distance from donor atom to acceptor atom? (Distances can be measured using Protein Explorer to view the final compact model only from the link above. In QuickViews, DISPLAY Distance.)

  2. How do the donor-to-acceptor distances in the water simulation compare with those in proteins?

  3. In the final (compact droplet) conformation, how many hydrogen bonds does each molecule donate? Accept?

  4. Why do some molecules participate in more hydrogen bonds than do others?

  5. In the final (compact droplet) conformation, how many molecules participate in the maximum number of hydrogen bonds that are possible for a water molecule?

  6. What is the geometric arrangement of the four bonds (two covalent, two noncovalent) in which a single oxygen atom may participate?

  7. What final (equilibrium) shape would the droplet adopt if it contained far more molecules?

  8. What term describes the force that compels the droplet into this shape, and resists deforming this shape?

  9. In molecular terms, what produces the above-mentioned force?

  10. Why is an oil droplet easier to deform than a water droplet?
Answers are available to teaching faculty who inquire with an email to emartz@microbio.umass.edu providing evidence of their faculty positions, such as by reference to a school or college website listing faculty.


10 water molecules were arranged arbitrarily in two approximately straight rows of 5, a bit farther apart than van der Waals radii. This initial arrangement could be thought of as a gas-like conformation (lacking entropy!).

Energy minimization was then applied, causing the molecules to collapse into a small droplet with ample hydrogen bonding. Energy minimization involved van der Waals interactions and electrostatics, and was done with MDL Sculpt. There is no thermal energy in this simulation.

24 frames of atomic coordinates were saved from the minimization process, which can be played as an animation.

For the first 11 frames, only van der Waals energies were applied. Starting with the 12th frame, both van der Waals and electrostatic interactions were utilized. This was done in order to produce a single droplet. When electrostatics were invoked from the outset, two droplets were formed. In the animations, the transition at the 12th frame produces a momentary reversal of the general trend towards compaction.

Feedback to Eric Martz.