[gmx-users] about rdf

[Moeed]

Hello,

1- In the manual I see rdf plot for Oxygen-Oxygen of SPC-water.  I think
this shows the average O-O density between all water molecules. I read a
post saying that rdf is calculating C_C distances for each C on chain 1 for
instance and all other C on the chain and other chains..
http://lists.gromacs.org/pipermail/gmx-users/2006-November/024831.html

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.

2- What doesy axis show? the average number density? ( I am calculating 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 read all
frames when I issue the command below even for only 2 chains having 60
ethylene units. Am I doing something wrong?

g_rdf -f *.trr -s *.tpr -o rdf -n *.ndx

Group     0 (      System) has  2896 elements
Group     1 (      PE60-1) has   362 elements
Group     2 (      PE60-2) has   362 elements
Group     3 (      PE60-3) has   362 elements
Group     4 (      PE60-4) has   362 elements
Group     5 (      PE60-5) has   362 elements
Group     6 (      PE60-6) has   362 elements
Group     7 (      PE60-7) has   362 elements
Group     8 (      PE60-8) has   362 elements

groups 1 to 8 each contain all C and H atoms in the molecule.

Thanks,
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