Hi Nidhi,
If I remember correctly (and your use of "p2" suggests so), that should be
the ensemble average of the 2nd-order Legendre polynomial of the angle
between the molecular axis and the membrane normal, right?
Although the order parameter computed by "gmx order" uses that same
definition, it takes each C-H bond of the aliphatic lipid tail, not the
overall molecular axis. So, "gmx order" is not what you want.
You can in principle compute what you need in two steps: (1) use "gmx
gangle" to compute the angle of interest for all molecules and all
snapshots (you will have to defined the vector of interest, say as the one
connecting the tail to the head); (2) do a small script to compute the
average from those data.
Best,
Antonio
On Tue, 30 May 2017, nidhi sorout wrote:
Dear All,
I want to calculate the nematic order parameter (p2) at each time step.
Is it possible to do this with "gmx order"?
If not than please suggest the right way.
Thank you,
Nidhi
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