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

raj vvindv.vvindv at gmail.com
Mon Sep 26 13:04:01 CEST 2011


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)

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?

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