Practical Free Energy Calculations

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Practical Free Energy Calculations

• Jesús A. Izaguirre
• izaguirr_at_nd.edu
• CSE 60531 Computational Biophysics and Systems
  Biology Spring 2006

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Outline
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Potential of Mean Force (PMF)
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(No Transcript)
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Slow Growth
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Jarzynskis Equality
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Jarzynskis Equality
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Jarzynskis Equality
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Exact PMF for decalanine
? A
?
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Extension vs. Time
?
t (ps)
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Force vs. Extension
F
?
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Work vs. Extension
W

?
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Work vs. Extension (Jarzynski)
W

?
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Configuration in NAMD

• conformational free energies
• 10 ps growing time as per NAMD user guide
  example
• use pulling speed of 0.1 A/ps as per NAMD
  tutorial, p. 68
• freeEnergy on
• freeEnergyConfig
• urestraint
• dist pmf (BH, 1, N) (BH, 10, NT) kf7.2
  low13 hi33
• pmf
• task grow
• time 10 ps
• pmf
• task up

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Configuration in NAMD

• time 200 ps
• print 1 ps
• pmf
• task stop
• time 10 ps
• pmf
• task down
• time 200 ps
• print 1 ps

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Outline
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ABF vs. Exact PMF
?
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ABF vs. Exact PMF
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Configuration in NAMD

• source ../NAMD_2.6b1_Win32-i686/lib/abf/abf.tcl
• abf coordinate distance
• abf abf1 4
• abf abf2 99
• abf dxi 0.2
• abf xiMin 12.0

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Configuration in NAMD

• abf xiMax 32.0
• abf outFile deca-alanine.dat
• abf fullSamples 500
• abf inFiles
• abf distFile deca-alanine.dist
• abf dSmooth 0.4

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References

• Tutorial Stretching Deca-alanine
  (http//www.ks.uiuc.edu/Training/Tutorials/)
• S. Park et al., Free Energy Calculation from
  Steered Molecular Dynamics Simulations Using
  Jarzynski's Equality, Journal of Chemical
  Physics, 1193559-3566, 2003.
• NAMD 2.6b1 Users Guide