Molecular Dynamics and Free Energy from Sampling · seed 1 · A4, ink-friendly. The answer key prints on its own page for grown-ups.

Running molecules and reading the average

Science · Chemistry · ages 23-24
Name ______________________   Date ____________

  1. You watch an average quantity as the run grows. What does a converged run look like?

    • A steady slope that never levels
    • A line that wiggles around a flat level
    • A value fixed from the very first step

  2. What does a thermostat do for a molecular dynamics run?

    • It holds the chosen temperature for the ensemble
    • It picks the starting positions of atoms
    • It removes the need for a force field

  3. Biasing along a chosen coordinate can produce a free energy profile.

    Circle one:   True   False

  4. Two runs of one binding event disagree. Which check separates a sampling problem from a force field problem?

    • Extend one run and also retry with a second force field model
    • Plot the same short run twice
    • Average the two runs and publish the middle

  5. A binding event is too rare to wait for. What do you do?

    • Lower the temperature until motion stops
    • Delete the barrier from the force field
    • Bias along a distance coordinate, then strip the bias in analysis

  6. A monitored average that still drifts steadily is converged.

    Circle one:   True   False

  7. A free energy profile reads 3 kilojoules per mole at state B and 12 at the top. How many kilojoules per mole does the return barrier from B measure? Type the number.

    Answer: ______________

  8. A student keeps extending a run, but every run with these charges misses the measured value. What is the verdict?

    • Sampling is still short, so extend further
    • The force field misleads, so the model must change
    • The thermostat picked the wrong atoms
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Answer key

For grown-ups. Fold this page away before handing over the rest.

Running molecules and reading the average W1-mt_ajdYrZOzEd-s1

  1. A line that wiggles around a flat level · Flat wiggle means converged, while drift means you extend the run.
  2. It holds the chosen temperature for the ensemble · The thermostat keeps the trajectory inside the ensemble the averages assume.
  3. True · The bias pushes over the barrier, and corrected counts become the profile.
  4. Extend one run and also retry with a second force field model · Longer time tests sampling, while a second model tests the force field.
  5. Bias along a distance coordinate, then strip the bias in analysis · Bias drives the rare crossing, and analysis removes its effect.
  6. False · A steady drift means the run needs more time.
  7. 9 · Subtract state B from the top: 12 minus 3 is 9.
  8. The force field misleads, so the model must change · Long runs that all miss together point to the force field, not sampling.
Worksheet · LightMySky