Hello,
I want to calculate RDF of glycine of Hn-OW, Hn-HW, Ha-OW, Ha-HW, Ca-OW, etc.,
So my commands were as follows...
1] To make indexes:-
gmx make_ndx -f md.gro -o Hn-OW.ndx
> del 2
Removed group 2 'SOL'
> del 1
Removed group 1 'Water'
> del 0
Removed group 0 'System'
> a H1 H2 H3 OW
Found xxx atoms with name H1 H2 H3 OW
0 H1_H2_H3_OW : xxx atoms
> q
2]Then, Using the index to calculate the pair correlation function for all frames:-
gmx rdf -f md.trr -s md.tpr -n Hn-OW.ndx -o rdf_Hn-OW.xvg
Available static index groups:
Group 0 "H1_H2_H3_OW" (xxx atoms)
Specify a selection for option 'ref'
(Reference selection for RDF computation):
(one per line, for status/groups, 'help' for help)
> 0
Selection '0' parsed
>cntrl+d
Last frame 1000 time 10000.000
Analyzed 1001 frames, last time 10000.000
3] View the plot:
xmgrace rdf_Hn-OW.xvg
and if i view the obtained graphs in xmgrace i am getting only two kinds of graphs...ie.,
(a) for Hn-OW,Ha-OW etc, graphs are same for OW end indexing and
(b) for Hn-HW,Ha-HW etc., graphs are same for HW end indexing..
My doubts are..
1)What is this only two kinds of graphs am i getting..?? ,
2)I hope the above procedure to get RDF ie., commands 1] gmx make_ndx....., 2] gmx rdf ..... 3] xmgrace..... are correct in accordance..
3)Or is there any mistake that i am doing..?? Can anybody rectify my mistakes if any..??
Thank you.
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