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

André Farias de Moura moura at ufscar.br
Tue Nov 20 11:27:43 CET 2012

the opening statement "from the statistical mechanical standpoint" means a
thorough sampling has been attained, so I do agree that the reference group
choice would matter for an every day situation. Thoroughness is not
for most complex systems we might be interested in.

On Tue, Nov 20, 2012 at 1:21 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

> 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
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> jalemkul[at]vt.edu | (540) 231-9080
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Prof. Dr. André Farias de Moura
Department of Chemistry
Federal University of São Carlos
São Carlos - Brazil
phone: +55-16-3351-8090

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