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.moh...@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.
>
>
> Thanks in advance for your comments
>
> Cheers
> Mohsen
>
>
>
>
>
> --
> *Rewards work better than punishment ...*
>



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