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

[Mark Abraham]

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-bounces at gromacs.org 
> [mailto:gmx-users-bounces at 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.warren at 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-bounces at gromacs.org 
> [mailto:gmx-users-bounces at 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-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 
> <mailto: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 
> 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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> 
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