[gmx-users] g_density, number density

Justin Lemkul jalemkul at vt.edu
Tue Oct 16 15:40:26 CEST 2012

On 10/16/12 7:55 AM, Ali Alizadeh wrote:
> Dear All users
> 1- When i use these commands for generating number density profile
> I see completely different results(in z direction, length in z
> direction is 8, number density versus of z)
> g_density -f md.xtc -s md.tpr -dens number -o  dens8.xvg -d z -symm -center
> It's trend is increasing(from z=0 to z=2 then decreasing(fall to zero,
> z= 2-5) and then increasing(z=5-7.5)
> g_density -f md.xtc -s md.tpr -dens number -o  dens8.xvg -d z
> But in the case,It's trend is decreasing(z=0-2.5) then
> increasing(suddenly to maximum, z=2.5-5) and then decreasing(z=5-8)

You're telling g_density to do two different things.  You got two different 
results.  I don't see that as odd.

> 2- Number density profile Should be symmetric?

Only if the system is symmetric.



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


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