Hi, 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. Thanks.
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 all? 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! Andrew DeYoung Carnegie Mellon University -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists