[gmx-users] Lattice distance for HII phase

Mohsen Ramezanpour ramezanpour.mohsen at gmail.com
Thu Nov 17 19:07:48 CET 2016

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

I chose SOL for both options g_RDF asked me for reference and calculating

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


*Rewards work better than punishment ...*

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