[gmx-users] Correction for the use of harmonic position restraints in Umbrella Sampling

[Billy Williams-Noonan]

Hi Gromacs Experts,

   I have generated some binding free energies using steered MD and
umbrella sampling.  I've done this using a variation of the method
described by Justin Lemkul in his tutorial.

   My question is this:  do I have to correct my PMF dG calculation for the
use of position restraints, or does *gmx wham* already take this into
account?  My dG values are consistently higher than experimental values so
I was hoping this could help explain why.

   Best regards,

Billy

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