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

Antonio Baptista baptista at itqb.unl.pt
Mon Aug 20 22:12:27 CEST 2018

```You didn't give us much info about your system, so I will assume that your
box is a rectangular prism and that all the cylinders are necessarily
oriented along the z axis (e.g., because they are "infinite"/periodic).
Since the center of mass (COM) of each cylinder must be a point on its
axis, you simply need to compute the COMs of each cylinder and then
compute any intended distances between their axes using just the xy
components.

On Fri, 17 Aug 2018, Shan Jayasinghe 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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>>> before
>>>>>>>> posting!
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>>>>>>>>
>>>>>>> --
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>>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> Best Regards
>>>>>> Shan Jayasinghe
>>>>>> --
>>>>>> Gromacs Users mailing list
>>>>>>
>>>>>> * Please search the archive at
>>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>>>>> posting!
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>>> or
>>>>>> send a mail to gmx-users-request at gromacs.org.
>>>>>>
>>>>> --
>>>>> Gromacs Users mailing list
>>>>>
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>>>>>
>>>>
>>>>
>>>> --
>>>> Best Regards
>>>> Shan Jayasinghe
>>>> --
>>>> Gromacs Users mailing list
>>>>
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>>>> posting!
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>>>>
>>> --
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>>>
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>>
>>
>> --
>> Best Regards
>> Shan Jayasinghe
>>
>
>
> --
> Best Regards
> Shan Jayasinghe
> --
> Gromacs Users mailing list
>
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>
```