I would like to calculate the time correlation of rotational diffusion using second rank Legendre polynomial.
I use the command as below:
vector v1 :1.C11 corr :1.C24 order 2
analyze timecorr vec1 v1 vec2 v1 tstep 1.0 tcorr 16000 drct norm out head-LIPID001-C11_C24.out
My doubt here is if the vector v1 is unit vector?
In one of the literature, (Biophysical Journal 87(5) 2976-2989), they used equation as below:
C_2(t) = 1/2 < 3(u(t)-u(0))^2 - 1>, where the "u" is the unit vector.
The clarification may help to use this method unambiguously.
note: If the vector is not unit vector, than how to proceed in calculating the C_2(t) in ptraj?
Thanks in advance,
Vijay Manickam Achari
(Phd Student c/o Prof Rauzah Hashim)
Chemistry Department,
University of Malaya,
Malaysia
vjramana.gmail.com
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Received on Thu Feb 13 2014 - 06:30:02 PST
