<br>Hello Justin,<br><br>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.<br>
<br>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? <br> (It takes much time and I wanted to know how it is calculated in gromacs). <br>
<br>Thank you for your help,<br><br><br>*******************<br><div class="gmail_quote"><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><br>
> Now I am trying to do the same thing to get rdf for C-C or C-H for<br>
> polymer chains. I looked into default index groups and I guess<br>
> Protein-H, BAckbone and Mainchain groups for my system should give only<br>
> carbon atoms (I have only polyethylene chains), and Non-Protein should<br>
> give only H. but I do not know how I can use them since System is the<br>
> only default group I see.<br>
><br>
<br>
Do you have protein molecules? If not, then you won't have default groups like<br>
Protein, Protein-H...<br>
<br>
> 2- What doesy axis show? the average number density? ( I am calculating<br>
<br>
Please use Google to answer this question.<br>
<br>
> rdf between chains 1 and 2 for instance. y-axis is in the range of 0-300<br>
> ?! and x-axis varies between 0-15 nm?!. normally g(r) is in the range of<br>
> 1 to 5 ..). and also I noticed it takes much time for the program to<br>
<br>
Normally? Based on what assessment? Unless you have exceptionally good<br>
sampling, your RDF plot probably won't converge very well for large molecules,<br>
especially if you are analyzing all possible atomic pairs.<br>
<br>
> read all frames when I issue the command below even for only 2 chains<br>
> having 60 ethylene units. Am I doing something wrong?<br>
><br>
<br>
No, but g_rdf is doing something on the order of 362*362 calculations, so you<br>
can count on that taking a lot of time (and memory).<br>
<br>
-Justin<br>
<br>
<br>
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