Molecular Dynamics Simulation

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Molecular Dynamics Simulation
http//www.math.iastate.edu/wu/math597.html
http//www.math.iastate.edu/wu/Math597HW0000

• Math/BCB/ComS597
• Zhijun Wu
• Department of Mathematics

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Computer Simulation of Molecular Motion
Physical Model
Mathematical Model
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Computer Simulation of Molecular Motion
Numerical Solution
Computer Simulation
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Computer Simulation of Molecular Motion

• Atomic Fluctuation
• Sidechain Motion
• Loop Motion
• Terminal Arm Motion
• Helix Motion
• Domain Motion
• Subunit Motion
• Helix-Coil Transition
• Coupled Structural Changes
• Distortional Fluctuation
• Folding and Unfolding

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Time Scales for Protein Motion
Bond vibration
Isomeris- ation
Water dynamics
Helix forms
Fastest folders
Typical folders
Slow folders
10-15 femto
10-12 pico
10-9 nano
10-6 micro
10-3 milli
100 seconds
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A Simple Example
potential energy
h (x)
h(x)
x
force field
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Newtons Equation
h (x)
h(x)
x
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Systems of Equations
h (x)
h(x)
x
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Numerical Solution
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x (t), x0 1, v0 0.5
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x (t), x0 1, v0 0.1
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(x (t), v(t))
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Initial Value Problem
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Boundary Value Problem