[gmx-users] problem with g_density

Justin A. Lemkul jalemkul at vt.edu
Mon Oct 25 12:57:26 CEST 2010

Ozge Engin wrote:
> 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 replied.
> I have attached the density profile in the attachment.
> Why is it the case?

The behavior at the box boundaries is identical to that of the middle of the box 
(10 nm), which indicates to me that all interfaces are acting equivalently, 
which should be reassuring, I would think :)  You're not seeing complete mixing 
of your two species, but there is some diffusion between the phases, otherwise 
both of your particles should drop to exactly zero density on either side of the 
box middle, wouldn't they?


> Regards
> -- 
> Ozge Engin


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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