[gmx-users] PMF calculation by umbrella sampling simulations

MPI mpi566 at gmail.com
Thu Apr 30 06:43:22 CEST 2015

 Dear Users,

  With GMX 4.6.5, I tried to reproduce a system of the dissociation of
a single peptide in an AB42 protofibril with PMF (potential of mean
force) calculation in Justin's umbrella sampling tutorial.  He
derived the binding energy from PMF from a series of umbrella sampling
simulations and obtained a value of  free energy  close to  -50.5
kcal mol-1.   But I got a value of -37.5 kcal mol-1 after PMF
curve was converged.  The value difference is significant and this
raises two questions.  What dose cause this difference of  ~13 kcal mol
-1  ?  although I used  GPU for calculations, which is the only
modification (cutoff-scheme = Verlet).  What is a reasonable range of
binding free energy in this case of AB42 protofibril ?

The umbrella histogram showing the overlap between window looks
reasonable. See attached here.


Suggestions or opinions are appreciated.


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