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

[André Farias de Moura]

Nidhi,

you need some background reading on the specifics of your problem/system
(including order parameters for liquid crystals and other orderly systems)
before you can do a meaningful modeling and that is up to you (it is your
research problem, not ours)

as I told you, the director makes sense only when you define that there is
some sort of anisotropy in your system, either raised by an external field
or by an interface. If you don't have any fields or interfaces (e.g. a free
protein tumbling in an aqueous solution) then any direction is equally
probable and a long enough simulation would average out to zero any order
parameter with respect to any arbitrarily chosen director (which is one of
the ways you may define what an isotropic solution is)

Andre

On Sat, Jun 3, 2017 at 3:09 AM, nidhi sorout <nidhi020191 at gmail.com> wrote:

> In my case for second  order parameter I need the angle between the unit
> vector linking N- and C-termini of the ith peptide and the  d (the
> director) is a unit vector defining the preferred direction of alignment.
>
> These vectors are not clear to me.. please suggest something.
>
>
> Nidhi
>
> On Sat, Jun 3, 2017 at 5:10 AM, André Farias de Moura <moura at ufscar.br>
> wrote:
>
> > 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
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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