[gmx-users] xy option in g_rdf
adeyoung at andrew.cmu.edu
Sat Feb 18 19:06:45 CET 2012
If you have time, I have a question about the -xy option in g_rdf. I'm a
little afraid that this may be silly question and the answer might be
obvious in hindsight, but I have been having difficulty finding the answer.
As we all know, g_rdf computes radial distribution functions of, for
example, atoms. With the default options, g_rdf I think computes what I
might naively call "three-dimensional" or "isotropic" radial distribution
functions. Borrowing a conceptual example from Benjamin Widom's
"Statistical Mechanics: A Concise Introduction for Chemists," I think that
we can think about the situation as follows. Suppose there is an atom at
some point O. The mean local density at a distance r from O is given by
(mean local density at a distance r from O) = rho*g(r)
where rho = N/V is the average number density at a distance r from O, and
g(r) is the RDF at r. So, basically, I think of a "three-dimensional" RDF
at r as being computed by looking at atoms located at the surface of a
(three-dimensional) shell of radius r centered at O, and then averaging over
both space and time (as described in section 8.4 in the Gromacs Manual).
But what happens if I use the -xy option in g_rdf? The manual page
(http://manual.gromacs.org/current/online/g_rdf.html) says that with -xy,
the RDF will be "calculated around axes parallel to the z-axis"; in other
words, only the x and y components are included in the computation. What
does this mean conceptually? Does it mean that instead of having a
(three-dimensional) shell of radius r centered at O, we now have a
(two-dimensional) RING of radius r centered at O? (This ring of radius r, I
guess, is parallel to the xy-plane.) Is the z-component averaged over at
Even if my guesses in the previous paragraph are correct, though, in general
when is the -xy option useful? If I have a solid surface parallel to the xy
plane and want to characterize the distribution of water molecules above
that solid surface, then the -xy option would NOT be useful in this case; is
this correct? On the other hand, if I have a carbon nanotube with its axis
along the z-axis and want to determine the distribution of water molecules
at distances radial from the nanotube axis, then the -xy option WOULD be
useful in this case; is this correct?
Or if you have time, can you please help me think of a conceptual example
that will help me visualize what the -xy option does?
Thanks so much for your time!
Carnegie Mellon University
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