[gmx-users] Re: gmx-users Digest, Vol 77, Issue 33

Moeed lecielll at googlemail.com
Tue Sep 7 18:22:18 CEST 2010

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.

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).

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
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