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

[Antonio Baptista]

On Sat, 3 Jun 2017, nidhi sorout wrote:

> 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'?

In your case, what does 'director' mean exactly?

>
> 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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