Indeed, they must be binary identical to each other, no matter what. I am sending two rdf plots for a lipid oxygen atom and water oxygen, plots are identical (lipids inside a spherical micelle). cheers Andre
On Tue, Nov 20, 2012 at 12:01 PM, Thomas Schlesier <schl...@uni-mainz.de>wrote: > The rdf should not depend on the choice 'which is group A and which is > group B'! Not if the system is well equilibrated and not if you consider > only a single snapshot (in that case the rdf looks like garbage if the > system is not really huge, but the RDF(A-B) and RDF(B-A) must be the same). > > I mean the the RDF is the radial distribution function. A distribution > about distances, and in distances one has no information about direction, > or from which point one goes to another. > In an A and B system one has N_A * N_B distances, no matter if A or B is > the reference! > > Going to the manual the given equation for the RDF is > > g(r) = 1/rho_B 1/N_A sum_A sum_B delta(r_AB - r) / (4pi r^2) > > Since after the sums it is clear that there is no difference between A and > B one could argue that > > 1/rho_B 1/N_A is not equal to 1/rho_A 1/N_B > > looking into the picture which defines rho one recognises that rho=N/V > > -> g_AB(r) = g_BA(r) > > > Am 20.11.2012 12:00, schrieb gmx-users-requ...@gromacs.org: > >> 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 >> attainable >> for most complex systems we might be interested in. >> >> On Tue, Nov 20, 2012 at 1:21 AM, Justin Lemkul<jalem...@vt.edu> wrote: >> >> > >>> > >>> >On 11/19/12 10:04 PM, Andr? 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 >>> > >>> >> > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > * Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > > -- _____________ 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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