Shan,

Load the .gro file into VMD , select the atoms/residues  of interest    see:  
https://www.youtube.com/watch?v=QV0_CJHBF6U  

For a plot , You could try converting the trr file to text readable format with 
trjconv.  From there select the atom numbers from each micelle that represent 
the center.  Then you write a small script in R to plot the difference between 
centers.  

Paul

> On Aug 11, 2018, at 5:26 AM, Mark Abraham <mark.j.abra...@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 <shanjayasinghe2...@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.abra...@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 <
>> shanjayasinghe2...@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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