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.
-Justin
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
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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