[gmx-users] free energy

Gavin Melaugh gmelaugh01 at qub.ac.uk
Wed May 4 17:51:52 CEST 2011

Hi Chris

My windows are restrained obviously using the force constant in the mdp
file. The trajectories that I have viewed are those of the individual
biased sampling windows. I have not put on the unbiased simulations yet.
There is also the following issue: The simulations involve two identical
molecules containing hydrocarbon chains. I calculate the PMF to take a
specific hydrocarbon chain of one molecule out of a specific site on the
neighbouring molecule. When this guest chain goes out, other chains can
go in (intramolecular or intermolecular). Will this affect the profile?


chris.neale at utoronto.ca wrote:
> 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.
> Chris.
> -- 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?
> Cheers
> Gavin

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