[gmx-users] Correction for the use of harmonic position restraints in Umbrella Sampling
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.
Billy Noonan* | *PhD Student *|* Bsci ( *Adv* ), IA Hon
**|* +61420 382 557
Monash Institute for Pharmaceutical Sciences ( *MIPS* )
Royal Parade, Parkville, 3052
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