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

[nidhi sorout]

Thank you all..
I am a newly research scholar that's why taking some time in understanding
:)
I will try again..

Nidhi

On 3 Jun 2017 7:49 p.m., "André Farias de Moura" <moura at ufscar.br> wrote:

> 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
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