[gmx-users] free energy perturbation

Anton Feenstra feenstra at chem.vu.nl
Tue Oct 28 09:01:05 CET 2003

Yuhua Song wrote:
> When I use "g_energy -f 1.edr -f2 2.edr -fee -s 1.tpr" to get the
> runavgdf.xvg about the free energy information. The first coloumn shows the
> time, the second coloumn shows the the potential energy difference between
> two states: E1-E2, the third couloum shows the free energy differnce, my
> understanding is right?

I suppose so. It is some time since I used this option. The .xvg file should
describe which set of values is what (check the 'legend' lines, or load it in
xmgr/xmgrace). If all else fails, you could check the source code of g_energy ;-(

> My question is: then what will be the difference for geting the free energy
> perturbation with the thermodynamics integration way? because thermodynamics
> Integration way will involve at least another 2ns calculation. If there is
> no advantage for thermodynamics integration way, then why bother to use TI
> way to get free energy perturbation other than the way using the
> mdrun -rerun way?

The 'mdrun -rerun' way is known as Free Energy Perturbation, which already gives
a hint: the modification must be small enough to be considered a perturbation.
More to the point, the ensembles of both states must show enough overlap such that
averages calculated over the ensemble from one state (i.e. the trajectory), with
the interactions (i.e. the .tpr file) of the other state, and vice versa give
the same average. This need not be the case for any arbitrary modification.

A good example of an 'FEP'-able modification is the difference between ground-state
and exited state (as in photon-absorption) FAD (flavin-adenine-dinucleotide, a
fluorescent, self-quencing molecule that is the co-factor to flavin proteins).
This difference is well described by a slight shift in charge distribution on
a three-membered aromatic ring system (see J. Phys. Chem. B 106, 8858-8869, 2002).


  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |

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