[gmx-users] LIE interaction energy calculations

[Anton Feenstra]

Bert de Groot wrote:
> 
> Hi,
> 
> if your sampling is good enough, you can obtain a good estimate of
> the relative free energies by "counting", and forget about the MD
> energies. Eliminate the bias caused by the choice of starting
> conformations, and directly calculate the free energies from the
> configurational densities (G=-kT ln (rho)) evaluated along properly
> chosen coordinates (either on a grid or using a nearest neighbors
> approach). We did this for the Daura et al reversible peptide folding
> simulations and got a useful estimate of the folding/unfolding free
> energy landscape:
> 
> Bert L. de Groot, Xavier Daura, Alan E. Mark and Helmut Grubmüller;
> Essential dynamics of reversible peptide folding: Memory-free
> conformational dynamics governed by internal hydrogen bonds;
> J. Mol. Biol., 390 (1): 299-313 (2001)

Good idea, but unfortunatly I don't sample the binding/unbinding.
I have a separate 'unbound' simulation of the ligand in water, and
several bound simulations of the ligand in the active site. I could
still get the relative free energies by counting the population of 
the different binding modes, though, but I'm not sure if that helps.


-- 
Groetjes,

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