[gmx-users] Re: Strange form of RDF curve

[Justin Lemkul]

On 11/19/12 10:04 PM, André Farias de Moura wrote:
> from the statistical thermodynamics standpoint, rdf must be the same for
> both choices of reference group, i.e.,solute-solvent and solvent-solute
> must yield exactly the same rdf, the only difference being expected for the
> cumulative numbers, which depend on the particles number density. The
> reason why rdf's must be the same is the fact that rdf are connected to the
> pmf between the particles, and the pmf do not depend upon the choice of
> reference group, just on the reaction coordinate connecting the groups.
>

Doesn't this explanation assume that the system is homogeneous, or at least, 
that the solute (reference group) of interest exhaustively samples 
configurations within the solvent?  It's not intuitive to me why one would 
expect an Arg-water RDF to be the same as a Water-Arg RDF when the Arg residue 
is only part of a 582-residue protein, which means a considerable portion of the 
simulation unit cell contains neither the Arg of interest nor water, a fact that 
significantly impacts the binning as shown in the manual.  The actual g_rdf 
command is essential in this regard, as well, depending on how the RDF is being 
calculated.  One can produce wildly different results by changing only a a 
single element of the command.

-Justin

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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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