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

[André Farias de Moura]

Hi Nidhi,

In short: you are using a general-purpose software, so it does not have
tools for all specific applications any user might be interested in. Either
you have to hack/adapt existing analysis tools or you have to write your
own tools.

That being said: the director is a rather arbitrary direction even
experimentally, it becomes well-defined only when you have an external
field (usually magnetic or electric, maybe both) or an interface, so the
director would be either the direction of the field or the direction
perpendicular to the interface, respectively.

Anyway, it is up to you to decide which direction makes sense as the
director of your system. Once you choose that vector and a vector defining
what you are naming "molecular axis", calculating angles and correlation
functions to obtain any sort of order parameter can be accomplished
straightforwardly using any spreadsheet.

(pretty much the same Antonio had already told you)

Andre

On Fri, Jun 2, 2017 at 6:21 PM, nidhi sorout <nidhi020191 at gmail.com> 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'?
>
> 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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-- 
_____________

Prof. Dr. André Farias de Moura
Department of Chemistry
Federal University of São Carlos
São Carlos - Brazil
phone: +55-16-3351-8090