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

Billy Williams-Noonan billy.williams-noonan at monash.edu
Tue Aug 16 09:24:40 CEST 2016

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 Noonan*    |    *PhD Student    *|*    Bsci ( *Adv* ), IA Hon

*LinkedIn Profile
**|*   +61420 382 557

Monash Institute for Pharmaceutical Sciences ( *MIPS* )
Royal Parade, Parkville, 3052

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