[gmx-users] problem with g_density

Ozge Engin ozge.engin at gmail.com
Mon Oct 25 12:52:47 CEST 2010

Hi all,

I have some difficulties with understanding the output of g_density command.
I have a system composed of two Lennard Jones particles, A and B in a
20.712x20.712x20.712 simulation box. The parameters between the two
particles are given such that they do not mix, but they undergo a phase
separation. I want to investigate the density profile of the system, and  I
used the following command line to do that:

g_density -f traj.xtc -n index.ndx -dens number -sl 100

The density profile for the two types of particles looks OK except the
boundaries of the simulation box. I mean I would not expect to get a number
other than 0 at the lower and upper boundaries. I have also searched the
mailing list. There was an e-mail similar to that one, but it was not

I have attached the density profile in the attachment.

Why is it the case?


Ozge Engin
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