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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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
definitio
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" wrote:
> Hi Nidhi,
>
> If I remember correctly
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?
Nidh
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 dir
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
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
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" wrote:
> Nidhi,
>
> you need some background reading on the specifics of your problem/system
> (including order parameters for
