[gmx-users] about rdf

Justin A. Lemkul jalemkul at vt.edu
Tue Sep 7 18:28:26 CEST 2010

Moeed wrote:
> Hello Justin,
> 1- Actually since I was focusing on rdf for C-C I didnt explain my 
> understanding from that post well. Anyway, I have only C and H in the 
> system and no protein. You mean I have to make separate groups of C and 
> H for all polymer chains by hand? I trying to find a more smart way of 
> doing this.. for big polymers doing this by hand is really awful.

Simply defining "C" and "H" is relatively meaningless, isn't it?  You have a C60 
chain, so you have 30 "different" types of C based on the symmetry of the 
molecules.  Perhaps you need to refine what it is you're looking to analyze. 
For large molecules, you will likely need exceptional sampling to get a nicely 
converged RDF plot.  I don't know how long that might take, but tens (if not 
hundreds) of ns might be necessary.

> 2- I dont see much information about structure factor in the manual or 
> in the archive. When I  use -sq option of g_rdf  it asks for index 
> groups. Does it make sense to define structure factor for a single chain?
>  (It takes much time and I wanted to know how it is calculated in gromacs).

I've never used this option, but if you want to know what it's doing, that's why 
the source code is publicly available.


> Thank you for your help,
> *******************
>      > Now I am trying to do the same thing to get rdf for C-C or C-H for
>      > polymer chains. I looked into default index groups and I guess
>      > Protein-H, BAckbone and Mainchain groups for my system should
>     give only
>      > carbon atoms (I have only polyethylene chains), and Non-Protein
>     should
>      > give only H. but I do not know how I can use them since System is the
>      > only default group I see.
>      >
>     Do you have protein molecules?  If not, then you won't have default
>     groups like
>     Protein, Protein-H...
>      > 2- What doesy axis show? the average number density? ( I am
>     calculating
>     Please use Google to answer this question.
>      > rdf between chains 1 and 2 for instance. y-axis is in the range
>     of 0-300
>      > ?! and x-axis varies between 0-15 nm?!. normally g(r) is in the
>     range of
>      > 1 to 5 ..). and also I noticed it takes much time for the program to
>     Normally?  Based on what assessment?  Unless you have exceptionally good
>     sampling, your RDF plot probably won't converge very well for large
>     molecules,
>     especially if you are analyzing all possible atomic pairs.
>      > read all frames when I issue the command below even for only 2 chains
>      > having 60 ethylene units. Am I doing something wrong?
>      >
>     No, but g_rdf is doing something on the order of 362*362
>     calculations, so you
>     can count on that taking a lot of time (and memory).
>     -Justin


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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