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

Enemark Soeren chees at nus.edu.sg
Wed Oct 21 11:28:04 CEST 2009

Hi Omer,

Thanks for your input.


Let me reformulate my problem:


I have glycine molecules in the form of zwitterions:



    1ZGLY     N    1   0.560   0.337   0.388 -0.0759 -0.2488 -0.5471

    1ZGLY    H1    2   0.625   0.312   0.461  0.6035  0.5922 -0.4315

    1ZGLY    H2    3   0.601   0.311   0.299  0.1500 -0.3357 -1.5372

    1ZGLY    H3    4   0.553   0.433   0.388  0.5086  2.8817 -1.8023

    1ZGLY    CA    5   0.426   0.272   0.403  0.3095  0.1790 -0.0455

    1ZGLY   HA1    6   0.352   0.335   0.345 -0.9032  0.4782  0.1366

    1ZGLY   HA2    7   0.433   0.173   0.358  0.7875  0.5369 -3.0389

    1ZGLY     C    8   0.378   0.267   0.551  0.1816 -0.4672  0.1868

    1ZGLY   OC1    9   0.449   0.218   0.644 -0.2820 -0.4080  0.2048

    1ZGLY   OC2   10   0.263   0.320   0.559 -0.0662 -0.2935 -0.8010



Now, I am interested in the interaction between the amine group hydrogen
atoms (H1, H2, and H3) and the water oxygen atom. Thus, I define 2 group
in an index file:

1.       aH1H2H3 (which contains all H1, H2, and H3 atoms in the glycine
molecules in my system)

2.       aOwat (which contains all oxygen atoms in the water molecules
in my system)


However, I also tried setting up a different index file with the groups:

1.       aH1 (which contains all H1 atoms in my system)

2.       aOwat (like before)


I find that these 2 index files do not produce the same RDFs. Why is



Best regards,



From: gmx-users-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org] On Behalf Of Omer Markovitch
Sent: Wednesday, October 21, 2009 4:27 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] g_rdf and number of atoms to include


On Wed, Oct 21, 2009 at 07:28, Enemark Soeren <chees at nus.edu.sg> wrote:

Dear users,

I would like to compare interactions between molecules by using RDF. I
have tried looking at glycine and water, and compare the following two

1)      between the amine hydrogen atoms in glycine and the oxygen atom
in water

2)      between the carboxyl oxygen atoms in glycine and the oxygen atom
in water 

However, my result in 1) depends on how many of the 3 hydrogen atoms I
include in the calculations. Why is that?

If you mean that when focusing your RDF calculations on either one of
the three hydrogens results in three different RDFs then it means that
each hydrogen feels water differently. I bet this difference is only for
the first peak of g(r) and the other peaks overlap between the three
RDFs. As for how reasonable this result, its not unlikely because
glycine has atleast 2 different types of hydrogens (say, C-H vs. N-H),
depending on the protonation state. You might want to provide more
details on the system you are studying to get better answer.
I am assuming that the RDFs are converged so that including more
trajectory data and/or sampled molecules and/or changing bin size does
not result in a drastic change to the curves.


	Does that mean that I cannot directly compare the strengths (RDF
peak height) of the two interactions as they are not based on the same
number of atoms? Does it also mean that I must always calculate RDFs by
using 1 atom on each of the particles/groups that I am comparing?

I am not sure how good it is to use the first peak of g(r) to analyze
strengths, but you should also consider the width and area under peak.
This peak is an average on all nearest neighbours, bonded or not, so it
might not give you a good estimate of the hydrogen bond, for example.
If you are unsure of your g(r) calc it just for water (that is - only
oxygen-oxygen of water-water). At long distances (~10 Angstroms) it
should fluctuate around 1.

Bests, Omer Markovitch. 


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