Thanks Mark and Omer for your comments - I have really learning a lot on RDF today based on your input!
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Omer Markovitch Sent: Thursday, October 22, 2009 3:49 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] g_rdf and number of atoms to include On Thu, Oct 22, 2009 at 05:17, Enemark Soeren <ch...@nus.edu.sg> wrote: Ahh, now I understand - sorry, Omer! No problem, glad to help. In fact, I have compared all three single hydrogen RDFs and they are identical and also relatively smooth. Since, however, with 3 times more data points (all three hydrogen atoms taken together) I get a different RDF, would that indicate that I do not have enough data after all? See my previous answers for some checks you can do on the convergence. You have to look at your data and decide if the differences are acceptable by you. I could suggest, for example, RMSD between curves, focusing just on the first peak. Are RDFs known to be slow to converge? A wild answer would be no, but thats basically depends on the size of your bin. A bin of 0.5 Angstroms would mean in each bin you'll probably have "enough" molecules for the data of this bin to converge, but than the curve itself wouldn't look smooth (even if it is converged). A bin size of 0.1 is often used. Without considering bin width before you mention it, I can see that I have been using a bin width of 0.02 Angstrom which is the default in Gromacs. Judging by your comment, this is quite a small bin width. However, I guess it explains why my curve looks smooth. This despite the RDFs not being converged. Thanks to Mark, I realized that my RDF for the 3 hydrogen atoms taken over only half the time does not reproduce neither my single hydrogen RDFs and even less my full production RDF with 3 hydrogens.. I am still a bit puzzled as to why this can happen, but I guess it clearly indicates that I do not have enough data for my bin width. I am trying to play around with this.. I have about 1000 water molecules and about 50+ glycine molecules, simulated for 10ns with 1ps sampling intervals. That should give me 500,000,000 data points for the distribution, right? Can I compare this number with the literature in which RDFs for, say, water-water interactions are reported? With 50 glycines you basically average 50 curves together, but the number of water molecules does not effect the statistics of the glycine RDF. The number of waters does mean that you most likely have a large enough system. As for water-water RDF, I think you should have more then enough data here. Just make sure when comparing to similar variables with the literature (potential, temperature, binning...). I would also worry about calculating my water-water RDF for a water which is close to glycine if I wanted to compare bulk water. One important point, which was not really clear to me before was if, provided that I have enough data, the RDFs should be identical no matter whether I use 1, 2, or 3 hydrogen atoms for generating the RDF. As far as I understood, both yours and Omer's responses indicate that the RDFs should be identical. Did I get that correctly? >From the top of my head I would say yes, you are correct. I recommend you look at some trajectory snapshots to make sure that indeed all 3 hydrogens have similar neighboring. Thanks for confirming that, Omer. Cheers, Omer.
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