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

Shan Jayasinghe shanjayasinghe2011 at gmail.com
Fri Aug 17 08:48:35 CEST 2018

```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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>> > > --
>> > > Gromacs Users mailing list
>> > >
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>> > >
>> >
>> >
>> > --
>> > Best Regards
>> > Shan Jayasinghe
>> > --
>> > Gromacs Users mailing list
>> >
>> > * Please search the archive at
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>
>
> --
> Best Regards
> Shan Jayasinghe
>

--
Best Regards
Shan Jayasinghe
```