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

André Farias de Moura moura at ufscar.br
Tue Nov 20 04:04:40 CET 2012

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.



On Mon, Nov 19, 2012 at 2:50 PM, shch406 <shch406 at bpci.kiev.ua> wrote:

> >I would have chosen the groups in the opposite manner.  You're interested
> in
> the
> >presence of water around the chosen arginine residue, not the presence of
> >arginine around water, right?  Given this order of chosen groups, the RDF
> seems
> >to make sense (very low probability that arginine is close to all water
> >molecules), though it doesn't represent what you likely want.
> >-Justin
> Of coarse, I'm interested in the presence of water around the arginine.
> But I did reverse order of groups, i.e. I toke water as the "1 group" and
> arginine sige
> chain tip as the "reference group", however have obtained absolutely the
> same curve.
> May be there exist some peculiarity in using g_rdf dialog to select groups?
> -Igor
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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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