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After the MD section you will: |
MD is a too time consuming process to set up a practical. If you want to try MD, you need to follow SFB in the third year. SFB contnues where this seminar series stops, and for SFB we get enough time to do some serious things, like a real MD simulation that we can go and let run for several days.
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Figure 54.
Molecular Dynamics, energy calculations, etc., are Force Field based
methods. The Force Field has been obtained from data in a very indirect
manner. To make things doable in human time, MD used Newton's laws of motion
where Quantum Chemistry should be used.
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Figure 55. Most Molecular Dynamics programs use a Force Field that consists
of 5 terms. Three are so-called trough-bond: bond lengths, bond angles, and
torsion angles. Two are through space: Van der Waals interactions and
electrostatic interactions. Many forces, though, are not included in these
Force Fields.
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Figure 56. Molecules don't fly through vacuum, but tend to swim around
in water. Therefore water must we present around the protein during MD
simulations.
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Figure 57. Time is of the essence in MD. MD is a trade-off between fast
calculations and more precise calculations. The time-step (typically on the
order of femto seconds) is thus a crytical component in any MD simulation.
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Figure 58. MD provides many opportunities, but it also knows a series of
severe limitations. Knowledge of those limitations, though, will help you
to use MD only for what it is good for.
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Figure 59. Midieval alchemists often tried to convert lead into gold. Today,
that is easy, in theory just take the editor and execute s/'Pb'/'Au'/. And
in MD it is not overly complicated either. Such conversions can be done (and the
energy involved calculated) using something called a thermodynamic cycle.
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