[gmx-users] Normalization in g_rdf

[Berk Hess]

Hi,

If you have N molecules with total volume which is significantly less than the unit-cell,
as is the case for ions in solvent, the RDF of the N molecules againt themselves
will converge to (N-1)/N.

Berk

> Date: Tue, 24 Nov 2009 01:27:27 +0100
> From: ondrej.marsalek at gmail.com
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Normalization in g_rdf
> 
> 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?
> 
> 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?
> 
> If these should work better than they do for me, I will of course
> check my simulations again. I would just like to check first if this
> is to be expected.
> 
> Thanks,
> Ondrej
> -- 
> 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
 		 	   		  
_________________________________________________________________
New Windows 7: Simplify what you do everyday. Find the right PC for you.
http://windows.microsoft.com/shop
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20091124/95b7bef9/attachment.html>