[gmx-users] Normalization in g_rdf
ondrej.marsalek at gmail.com
Tue Nov 24 13:23:30 CET 2009
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>
>> 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
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?
> gmx-users mailing list gmx-users at gromacs.org
> 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
More information about the gromacs.org_gmx-users