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

[nidhi sorout]

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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