AMBER Archive (2005)

Subject: Re: AMBER: Free energy extimate for the same structure but different conformers

From: David A. Case (case_at_scripps.edu)
Date: Mon Feb 21 2005 - 18:00:39 CST

On Mon, Feb 21, 2005, claudio wrote:
>
> I'd like to monitor the change in the free energy in function of time of
> a system containing about 1000 atoms in an explicit solvent with about
> 4000 TIP3P water molecules. There were no particular problems in the
> equilibration which went nicely up to 2ns. However, it might be
> interesting to plot along the same trajectory the change of free energy.
>

Note the free energy is not a mechanical quantity, so there is no
straightforward way to compute the free energy as a function of time; in this
sense it is very different than trying to plot the energy vs. time, or a bond
distance vs. time.

Note also that free energy is an *equilibrium* thermodynamic quantity,
so you need to be very careful or precise in thinking of it as a time
dependent quantity. You might think about dividing your simulation up into
"bins" of some length, and approximately estimating the free energy in each
bin (say with MM-PBSA). But in the absence of knowing what you wish to
do with this quantity, or exactly how it should be defined, it's hard to be of
further help.

...good luck....dac

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