[gmx-users] Lattice distance for HII phase
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 ~ =
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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