[gmx-users] atomic concentration in x and y axis

Mark Abraham Mark.Abraham at anu.edu.au
Mon Sep 26 15:00:43 CEST 2011

On 26/09/2011 9:04 PM, raj wrote:
> Hello,
> I have done simulations on cyclic peptide nanotubes and trying to 
> calculate the atomic concentration in the x and y axis, to measure the 
> diameter of the tube. I have tried using the g_rdf, but the results 
> are confusing to interpret. Here is the steps which I followed,
> 1. using trjconv, rotational and translational motions are removed 
> from the centered trajectory.
> 2. and then, g_rdf -f trj.xtc -s ref.gro -n index.ndx -o out.xvg  (I 
> understood that the "-rdf atom" option is the default one and this 
> will calculate the atomic distribution in the x and y plane)

You need to indicate that you want the 2D analysis with a specific 
option. Check out g_rdf -h


> I am not sure whether the elimination of translational and rotational 
> motions is enough to calculate this property, should I have to align 
> the structure in the z axis using the PCA analysis?
> Regards,
> Raj.

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