I am working one 36 chain fibril cross section. I want to calculate relative reorientation with respect to the center chain. For my simulation, I use position restrain in the center chain. I am little confused how I calculate relative reorientation (Δφ/Δr).
Dear Imrul,
I am not certain whether I understand correctly the idea, but from the formula you have provided, one could conclude that you want to calculate reorientation in terms of rotation! I suppose Δφ stands for angle between the axis corresponding to the initial position of the chain relative to the center, and the one that could be assigned after the reorientation. If so, you would probably need to calculate the distance between two representative positions of the central and the selected chain, before and after the reorientation. After that you will need to estimate the deviation between the initial and the final position of the selected chain, in terms of distance (which should correspond to Δr). I may be wrong, but it seems that the type of estimate closest to that is RMSD. Finally, the angle can be found with the law of cosines.
I agree with Tsvetan. You can use g_sgangle in order to evaluate the angle between each fibril chain, if you can consider each as a vector...I don't know really well your system, so you can consider it. And in order to evaluate the RMSD, you can use g_rms, with the first .gro position of your fibril chains as parameter in the -s flag.
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