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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