[gmx-users] from rdf -com to number density

Daskalakis Vangelis vdas.pilot at gmail.com
Sun Oct 18 15:08:34 CEST 2015

Hello all,
I run a simulation (NVT with a large box size) of a TIP4P water cluster
which assumes a spherical shape, as expected. I center this sphere in the
box throughout the trajectory. I analyze the trajectory with "gmx rdf
-com". I choose all waters as both the ref group and the second group. The
output xvg file contains the radials (from zero to half the box size every
0.002nm) along with the respective rdf values. The distribution seems ok in
shape (constant for radials from 0 up to somewhere close to my actual
sphere radial, and smoothly decreasing to 0 after that). At the constant
region I get a value of around 16. Is there a unit associated with this? Is
this the number density in nm-3? I guess not, as I would expect it to be
double this value (around 33 nm-3). How can I calculate the number density
p in nm-3?

Thank you a lot,
* <http://www.cut.ac.cy/est/staff/evangelos.daskalakis/>*


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