Enemark Soeren wrote:
Ahh, now I understand - sorry, Omer!
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?
Does your own data converge with itself as you go from half to 3/4 to
all of the data? That's a necessary (but not sufficient) criterion.
Are RDFs known to be slow to converge? 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?
How many data points at what interval do they have?
Mark
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?
Best regards,
Soren
*From:* gmx-users-boun...@gromacs.org
[mailto:gmx-users-boun...@gromacs.org] *On Behalf Of *Dallas B. Warren
*Sent:* Thursday, October 22, 2009 6:56 AM
*To:* Discussion list for GROMACS users
*Subject:* RE: [gmx-users] g_rdf and number of atoms to include
Omar’s response answered that question on why they are different. In
the first one you are grouping all three into one group, second is just
one of the hydrogen types. The fact that the rdf you get is different
indicates that all three hydrogens are not identical. Have you compared
the rdf for each hydrogen type individually? Another factor may also be
that in the first you have three times the number of data points, which
can smooth out the curves more.
Catch ya,
Dr. Dallas Warren
Department of Pharmaceutical Biology
Pharmacy and Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@pharm.monash.edu.au
+61 3 9903 9167
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble
a nail.
*From:* gmx-users-boun...@gromacs.org
[mailto:gmx-users-boun...@gromacs.org] *On Behalf Of *Enemark Soeren
*Sent:* Wednesday, 21 October 2009 8:28 PM
*To:* Discussion list for GROMACS users
*Subject:* RE: [gmx-users] g_rdf and number of atoms to include
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 that?
Best regards,
Soren
*From:* gmx-users-boun...@gromacs.org
[mailto:gmx-users-boun...@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 <ch...@nus.edu.sg
<mailto:ch...@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
interactions:
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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