[gmx-users] Re: Some additions to the free energy question.

[Anton Feenstra]

Markus O Kaukonen wrote:

> Is it not enought to first energy minimise structures (I and IE) and
> and then do the free energy pertubation for both
> 1) IE -> I'E
> 2) I  -> I'
> ?

IN the context of FEP, the perturbation does not involve simulation, but
merely a recalculation of perturbed energies. So, concrete, what you'd do is:
1) generate and minimize the IE and I'E complexes
2) md IE and I'E complexes (at least several ns...)
3) calculate perturbed energies, i.e. re-calculate energies of the "IE" traj
    using the "I'E" topology, and vice versa.

The assumption behind this is that differences are small enough to assume a
large amount of overlap in conformational space for both (I and I') states,
so that the IE generated ensemble (i.c. the traj), is also mostly applicable
for the I'E state.

> If you feel this of genereal interest, please forward to the list.

I do, and will.


-- 
Groetjes,

Anton
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|  _   _  ___,| K. Anton Feenstra                                     |
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