[gmx-users] Center to center distance in cylindrical micelles

[Dallas Warren]

z slices, then distance between center of mass of each rod, probably RDF to
get the ave over trajectory, then average across slices.

On Fri, 17 Aug. 2018, 4:48 pm Shan Jayasinghe, <shanjayasinghe2011 at gmail.com>
wrote:

> Hi All,
>
> Does anyone know how to calculate distance between two adjacent cylinders
> in a  hexagonal array?
>
> Thank you.
>
>
> On Sun, Aug 12, 2018 at 8:01 AM Shan Jayasinghe <
> shanjayasinghe2011 at gmail.com> wrote:
>
> > Hi,
> >
> > Actually, I want to calculate the lattice parameter (distance between two
> > cylinders) of hexagonal phase. Appreciate, if you could help me.
> >
> > Thank you.
> >
> >
> >
> >
> > On Sat, Aug 11, 2018 at 11:11 PM Mark Abraham <mark.j.abraham at gmail.com>
> > wrote:
> >
> >> Hi,
> >>
> >> A center is a point. I don't see how you would define a central point of
> >> an
> >> infinite cylinder.
> >>
> >> Mark
> >>
> >> On Sat, Aug 11, 2018, 14:47 Shan Jayasinghe <
> shanjayasinghe2011 at gmail.com
> >> >
> >> wrote:
> >>
> >> > Hi,
> >> >
> >> > I'm sorry for not providing the detail description of my system.
> >> Actually
> >> > it is a hexagonal phase. Therefore, four cylindrical micelles can be
> >> seen
> >> > in a cell. I want to calculate the center to center distance of two
> >> > cylindrical micelles.
> >> >
> >> > On Sat, Aug 11, 2018 at 8:35 PM Mark Abraham <
> mark.j.abraham at gmail.com>
> >> > wrote:
> >> >
> >> > > Hi,
> >> > >
> >> > > There is an axis of each cylinder but the two won't be parallel so
> >> there
> >> > is
> >> > > no unique distance to measure. So I suggest thinking carefully about
> >> what
> >> > > you really want.
> >> > >
> >> > > Mark
> >> > >
> >> > > On Sat, Aug 11, 2018, 06:58 Shan Jayasinghe <
> >> > shanjayasinghe2011 at gmail.com>
> >> > > wrote:
> >> > >
> >> > > > Hi,
> >> > > >
> >> > > > I tried to used gmx distance. However, I don't understand how can
> I
> >> > > define
> >> > > > the center of the circle face of the cylinder to the same in the
> >> other
> >> > > > cylindrical micelle.
> >> > > >
> >> > > > Can anyone help me?
> >> > > > Thank you.
> >> > > >
> >> > > >
> >> > > > On Sat, Aug 11, 2018 at 9:33 AM Mark Abraham <
> >> mark.j.abraham at gmail.com
> >> > >
> >> > > > wrote:
> >> > > >
> >> > > > > Hi,
> >> > > > >
> >> > > > > Have you looked at the different tools available and considered
> >> what
> >> > > > might
> >> > > > > be useful for you?
> >> > > > >
> >> > > > > Mark
> >> > > > >
> >> > > > > On Fri, Aug 10, 2018, 07:34 Shan Jayasinghe <
> >> > > > shanjayasinghe2011 at gmail.com>
> >> > > > > wrote:
> >> > > > >
> >> > > > > > Dear Gromacs Users,
> >> > > > > >
> >> > > > > > I want to calculate the center to center distance of two
> >> > cylindrical
> >> > > > > > micelles in my simulation. What gmx command should I use to
> >> > calculate
> >> > > > the
> >> > > > > > distance? Can anyone help me?
> >> > > > > >
> >> > > > > > Thank you.
> >> > > > > > --
> >> > > > > > Gromacs Users mailing list
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> >> > > > > --
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> >> > > >
> >> > > > --
> >> > > > Best Regards
> >> > > > Shan Jayasinghe
> >> > > > --
> >> > > > Gromacs Users mailing list
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> >> >
> >> >
> >> > --
> >> > Best Regards
> >> > Shan Jayasinghe
> >> > --
> >> > Gromacs Users mailing list
> >> >
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> >> --
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> >
> >
> > --
> > Best Regards
> > Shan Jayasinghe
> >
>
>
> --
> Best Regards
> Shan Jayasinghe
> --
> Gromacs Users mailing list
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