Hello,<br><br>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..<br>
<a href="http://lists.gromacs.org/pipermail/gmx-users/2006-November/024831.html" target="_blank">http://lists.gromacs.org/pipermail/gmx-users/2006-November/024831.html</a><br><br>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. <br>
<br>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?<br>
<br>g_rdf -f *.trr -s *.tpr -o rdf -n *.ndx <br>
<br>Group 0 ( System) has 2896 elements<br>Group 1 ( PE60-1) has 362 elements<br>Group 2 ( PE60-2) has 362 elements<br>Group 3 ( PE60-3) has 362 elements<br>Group 4 ( PE60-4) has 362 elements<br>
Group 5 ( PE60-5) has 362 elements<br>Group 6 ( PE60-6) has 362 elements<br>Group 7 ( PE60-7) has 362 elements<br>Group 8 ( PE60-8) has 362 elements<br><br>groups 1 to 8 each contain all C and H atoms in the molecule.<br>
<br>Thanks,<br><br>