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
--
========================================
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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