[gmx-users] free energy

Gavin Melaugh gmelaugh01 at qub.ac.uk
Wed May 4 16:38:17 CEST 2011

Hi all

I have performed a PMF simulation of taking part of a molecule out of
the cavity of a host using umbrella sampling. The free energy curve
suggests that the guest prefers to be outside the host as the bound
state is higher in energy, or the free energy difference to go in is
positive. However when I view the trajectories for each window it
appears that there is always more bound states than unbound. This leads
me to doubt my free energy profile?



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