Re: free energy methods cheat-sheet/comparison chart

From: Aron Broom (
Date: Mon Mar 25 2013 - 14:28:00 CDT

I don't have such a thing handy, and while there are certainly many
reviews, I can't think to name one off the top of my head. Are you
thinking very specifically or more broadly?

I would say in broad terms you're perhaps looking at two major classes of
simulations: those that attempt to sample across the whole reaction path,
i.e.: umbrella sampling, metadynamics, ABF, SMD, and so forth, and those
that attempt to examine just the two end states of interest, i.e.:
thermodynamic integration, FEP, MM/PB(GB)SA.

If you break it down like that, the pros and cons for those two big groups
are rather clear. For the whole reaction path methods, you'll be able to
generate, for instance, a PMF, and thereby not only get information on the
free energy difference between your two states of interest, but also the
kinetics from the energy barriers, or in other words, a real sense of the
actual pathway that is being followed. With the other class, you're really
just going to get the free energy difference, but, you'll be able to get it
faster (ideally).

I suppose there might also be some differences in efficiency depending on
your resources available. For instance, umbrella sampling involves many
isolated simulations (although you can also have temperature replicas for
each), so it's really well suited to parallelization across many different
machines if you have a lot of resources available, but not always in the
same place.

If you end up making such a cheat sheet, please share it! It's tough to
keep up with the development of all the new sampling methods for
determining free energy differences.


On Mon, Mar 25, 2013 at 2:49 PM, Thomas C. Bishop <> wrote:

> Does anyone happen to have a "cheat-sheet" with the pros and cons of the
> diff free-energy methods or a review that provides this information.
> Thanks in advance,
> TOm
> --
> *********************************
> Thomas C. Bishop
> Tel: 318-257-5209
> Fax: 318-257-3823
> **********************************

Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

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