[gmx-users] Normalization in g_rdf

[Berk Hess]

Hi,

g_rdf limits the distance to half the minimum periodic image distance.
So the volume normalization is always simply  4 pi r^2.
It uses the starting unit-cell with a factor of 0.99.
So you would only see strange effects when the box length reduces
more than 1% due to pressure coupling.

Berk

> Date: Tue, 24 Nov 2009 13:23:30 +0100
> Subject: Re: [gmx-users] Normalization in g_rdf
> From: ondrej.marsalek at gmail.com
> To: gmx-users at gromacs.org
> 
> On Tue, Nov 24, 2009 at 13:01, Omer Markovitch <omermar at gmail.com> wrote:
> >
> > On Tue, Nov 24, 2009 at 02:27, Ondrej Marsalek <ondrej.marsalek at gmail.com>
> > wrote:
> >>
> >> Dear all,
> >>
> >> I would like to understand better the way g_rdf performs
> >> normalization. I have two unexpected results:
> >>
> >> 1) In a simple simulation of atomic ions in water in a cubic box, I
> >> get RDFs that clearly reach a constant value at large enough
> >> distances, but that value is somewhat lower than one. The simulation
> >> is NpT, could that be a problem for the normalization?
> >>
> > g(r) should fluctuate around 1 at large distances, say 9 Angstroms for pure
> > water.
> 
> Indeed. However, see also Berk's remark. It seems to match very well
> for my system.
> 
> >
> >>
> >> 2) In a simulation in a dodecahedron, I get an unexpected decrease in
> >> the RDF at larger distances (for free ions in solution). Is there some
> >> know problem with normalization in triclinic cells? Is the RDF perhaps
> >> not truncated "soon" enough?
> >
> > Try calculating it for much larger distances, if you have PBC this should
> > not be a problem even with the current docecahedron.
> 
> Maybe I am missing something, but the range that g_rdf considers is
> hardwired - half the smallest box length with PBC, 3x the largest one
> without PBC. Is there a way to include contributions from multiple
> images of the unit cell?
> 
> BTW, if g_rdf really only considers the box edge lengths and
> disregards angles, it would make sense that normalization is broken in
> general cells at larger distances, no?
> 
> Ondrej
> 
> 
> > --Omer.
> >
> >
> > --
> > gmx-users mailing list    gmx-users at gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before posting!
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >
> -- 
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
 		 	   		  
_________________________________________________________________
Express yourself instantly with MSN Messenger! Download today it's FREE!
http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20091124/9aa514e8/attachment.html>