[gmx-users] g_rdf and number of atoms to include

Omer Markovitch omermar at gmail.com
Thu Oct 22 09:49:03 CEST 2009

On Thu, Oct 22, 2009 at 05:17, Enemark Soeren <chees at 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.

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.

Cheers, Omer.
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