[gmx-users] g_energy -fee -f2

[Anton Feenstra]

Xavier Periole wrote:
> 
> You ractually have to run two simulations. One would be the reference state
> (A)
> and the other is the perturbated state (B). g_energy calculate the free
> energy difference
> between the two states A and B. G_energy does not generate the perturbation.

The way I have used this option is to look at free energy differences
in conformations between a ground-state (GS) and excited-state (XS)
fluorophore (FAD). In this case I ran two simulations, one with GS charges
on the FAD, and one with XS charges. Then, I did four re-runs: GS trajectory
with GS tpr, GS traj with XS tpr, XS traj with GS tpr and XS traj with FS tpr.
(The 'GS traj/GS tpr' and 'XS traj/XS tpr' re-runs seem unnecessary, but
there are slight differences in total energies calculated between 'original'
and 're-run' that are elminated when all energies come from re-runs.)
This gives an estimate of the delta-delta-G, i.e. the difference in free
energy difference between two transitions (e.g., GS charges -> XS charges in
one ensemble, or GS ens. -> XS ens. in one charge state).


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| 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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