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

[nidhi sorout]

Hello,

Thank you Antonio..

But my angle of interest is the angle between the molecular axis of protein
and the director. I am not able to understand here, from where I can choose
this 'director'?

Nidhi

On 30 May 2017 8:55 p.m., "Antonio Baptista" <baptista at itqb.unl.pt> wrote:

> 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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