[gmx-users] Density profile

Alexander Alexander alexanderwien2k at gmail.com
Fri Apr 29 15:20:43 CEST 2016

Dear Gromacs user,

My system is a metal surface with thousands of Water molecule on it,
normally surface(3 nm) is in the bottom of the box and the rest on top is
water(6 nm). My target is to plot "density profile" of either WATER or OW
or HW along to Z(Normal distance above solid surface); 5 ns NVT simulation

1. "gmx density" has offered many options, I am not sure which I have to
choose to do so for this system, so, what is the right command to get this
density profile:
Mine is below , would you please improve it? I do not know why mine is
never like what I see in publications.

gmx density -f nvt.trr -s nvt.tpr -n surf-sol.ndx -d Z -dens number -b 500
-o HWdens.xvg

2. What is the "Relative density profile" which I see in some publications
usually? Relative to what it is?

3. What is the difference between "radial distribution function" and
"density profile" especially for such a goal?

Thanks in advance,

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