The gromacs manual says that the order parameter is calculated by inputting the angle between a vector and the z axis into an equation. So, if I would like to calculate the order parameter of the carbon backbone of polystyrene, is it true that I have to create two separate groups containing two different types of carbon atoms in the index file (because in one repeat unit of PS, there are two different carbon atoms)? And if it is so, will the final result show a plot of the order parameter as a function of distance in the z direction?
You need as many index groups as you have carbons in the chain. That will be many more than just two. The order parameter for carbon N in the chain is determined from a local axis of the carbon at positions (N-1) and (N+1). Thus every carbon in a chain is unique, even if they have the same atom name. Name is irrelevant; chain position is what matters.
Thank you for your answer. In fact, I do not understand what is the N. I have attached a text file containing what appeared in the terminal window. Is this N the "First atomnr"? Obviously, my calculation will be messed up if N is "First atomnr". How can I make N=1 for First atomnr = 13, N=2 for First atomnr = 16, so on and so forth?
N is the carbon number along the chain. It is not necessarily related to topological numbering, name, or global atom number within the coordinate file. The output provided indicates that you have almost what you need already - I don't know what C21, C31, C41, and C51 are, but if they're not part of the polymer backbone, you shouldn't be using them as index groups.
Thank you for your help. C21, C31, C41, C51 are in fact the n-butyl end group.
Hi,
I want to do the similar thing and use g_order, but I have problem with my index file. I have the index file for interesting part of one chain of 1 molequle(see below). How can I make that for all molequles in my box? I mean, what should I do to include all needed carbons in my box?
the index file is :
[ :_C3 ]
3
[ :_C5 ]
5
[ :_C6 ]
6
[ :_C7 ]
7
[ :_C8 ]
8
[ :_C9 ]
9
[ :_C10 ]
10
[ :_C11 ]
11
[ :_C12 ]
12
when I use g_order results in such comment:
Groupname: :_C3 First atomname: C3 First atomnr 2
Groupname: :_C5 First atomname: C5 First atomnr 4
Groupname: :_C6 First atomname: C6 First atomnr 5
Groupname: :_C7 First atomname: C7 First atomnr 6
Groupname: :_C8 First atomname: C8 First atomnr 7
Groupname: :_C9 First atomname: C9 First atomnr 8
Groupname: :_C10 First atomname: C10 First atomnr 9
Groupname: :_C11 First atomname: C11 First atomnr 10
Groupname: :_C12 First atomname: C12 First atomnr 11
As you see , not all needed carbons are counted. what should I do to include all needed carbons in my box?
Thanks in advance
Negar
I don't know how you created the groups in the index file you have now, but it is very simple to do this by atom name, e.g.:
> a C3
> a C5
> a C6
(etc)
as shown at http://www.gromacs.org/Documentation/Gromacs_Utilities/g_order
Assuming only molecules that you want to analyze have those atom names, it is just that simple.
I am studying orientation of carbons near water-triglyceride interface. I understood that I can calculate the order parameter for a especific carbon in achain, lets say c5, as a function of box length. For that matter I use :
g_order -f traj_solv_npt.trr -s tri_solv_npt.tpr -n sn1_c5.ndx -sl 40 -szonly -d z -b 900 -e 1000 -os orderfinal2.xvg
and my index file is attached.
My results were not what I expect. Can you please let me know if at least I use g_order for my propose structurally correct?
I appreciate your remarks. Thank you!
Presumably, but "not what I expect" doesn't give me much to go on in terms of seeing if there might be something wrong. Syntactically, I suppose it's fine, but I have never done anything like that. The gmx-users mailing list is probably a better forum for such a question. g_order issues similar to this one have been discussed in recent days.
Just curious. If I would like to calculate the order parameter of certain chemical group, such as the phenyl groups of polymer, can I use g_order to do so? Obviously, these chemical groups are not the same as the atoms in the C-C backbone. Also, in the program, do you think I can obtain the exact value of the angle? I know it is calculated from the cosine function, but angles of zero degree and 180 degrees would give the same order parameter. If you consider the orientation of these chemical groups at the surface/ interface, you would have no idea if these groups are pointing towards the surface/interface.
g_order specifically calculates deuterium order parameters, so it assumes all carbons are tetrahedral and consecutive. If you want to calculate other types of order parameters, you'll have to look into different programs or write your own code. The output of g_order on phenyl groups would be complete nonsense, if the program even ran.
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