# [gmx-users] Lattice distance for HII phase

Mohsen Ramezanpour ramezanpour.mohsen at gmail.com
Tue Dec 6 17:41:53 CET 2016

``` For whom this might have been a question:

Given a HII phase with cylinders parallel to z direction, simulation box
size in x and y-direction will give the cell size the lattice distance
(d_hex), respectively.

Cheers
Mohsen

On Thu, Dec 1, 2016 at 11:20 AM, Mohsen Ramezanpour <
ramezanpour.mohsen at gmail.com> wrote:

> Dear gromacs users,
>
> I appreciate your opinion on this email in advance.
>
> Cheers
> Mohsen
>
> On Thu, Nov 17, 2016 at 11:07 AM, Mohsen Ramezanpour <
> ramezanpour.mohsen at gmail.com> wrote:
>
>> Dear Gromacs users,
>>
>> I have a HII phase made of molecules. HII phase is formed of many
>> cylinders parallel to z axis (in my case) in a hexagonal geometry.
>>
>> I am interested in calculating the distance between these cylinders. I
>> want to have a more accurate statistical way to measure it. So, I think
>> radial distribution function is the good choice to do so.
>>
>> I used this command:
>>
>> gmx  rdf   -s  md.tpr    -f   md-whole.xtc   -n  index.ndx   -o  RDF.xvg
>>   -xy
>>
>> I chose SOL for both options g_RDF asked me for reference and calculating
>> RDF.
>>
>> md-whole means I treated PBC with "whole" option and then did this
>> analysis.
>>
>> The profile I got is not what I see by visualization.
>>
>> I think RDF will give alpha which is the unit cell size, but lattice
>> distance (d_hex) can be calculated by a simple calculation.  Alpha ~ =
>> (2/1.73) d_hex
>>
>> I am not sure if this is the right way or I should use other tools to get
>> the right values for this.
>>
>>
>>
>> Cheers
>> Mohsen
>>
>>
>>
>>
>>
>> --
>> *Rewards work better than punishment ...*
>>
>
>
>
> --
> *Rewards work better than punishment ...*
>

--
*Rewards work better than punishment ...*
```