Free Energy of Conformation Change

From: Arturas Ziemys (ziemys_at_chbmeng.ohio-state.edu)
Date: Mon Mar 12 2007 - 13:16:57 CDT

Hi,

I want to calculate the PMF of two amino acids in my protein. I suppose "Free Energy of Conformation Change" method should be used.

I guess dU corresponds to the total energy of the system. Am I right? I want to use just the interaction energy between those two amino acids to calculate PMF. Is there any way to control what energy PMF uses (like PairInteractions', etc.) ?

Is there any reference for "Free Energy of Conformation Change" method used in NAMD ?

best
Arturas

P.S. Below my script:

freeEnergy on
freeEnergyConfig {

urestraint {
  dist pmf (A,85,CA) (A,117,CA) kf=50, low=7.0, high=14.0
}

pmf {
  task = grow
  time = 10 ps
  print = 1 ps
}
pmf {
  task = up
  time = 500 ps
}
pmf {
  task = stop
  time = 10 ps
}
pmf {
  task = down
  time = 500 ps
}

}

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