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

Shan Jayasinghe shanjayasinghe2011 at gmail.com
Sun Aug 12 01:01:31 CEST 2018

```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.
> > > > > > --
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> > > > --
> > > > Best Regards
> > > > Shan Jayasinghe
> > > > --
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> > --
> > Best Regards
> > Shan Jayasinghe
> > --
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--
Best Regards
Shan Jayasinghe
```