[gmx-users] free energy

chris.neale at utoronto.ca chris.neale at utoronto.ca
Wed May 4 17:34:27 CEST 2011

Your windows are restrained. The PMF that you get out of WHAM is a  
representation of the relative sampling after removing the umbrella  
biases. Sounds like you are saying that you look at the still-biased  
trajectories and you see different a different distribution of states  
than you do in the de-biased PMF..... not sure what the problem is  
here. Perhaps go back to some review literature on US.

Now, if you saw more bound than unbound in unrestrained simulations,  
then that's a different story, but that doesn't appear to be what you  
are talking about.


-- original message --

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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