[gmx-users] Calculation of nematic order parameter using gromacs

Antonio Baptista baptista at itqb.unl.pt
Tue May 30 17:25:41 CEST 2017

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.


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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