Hi,
It looks like you do have the density for the water in your output
file - it's in columns 4 (average) and 5 (standard deviation):
#density :Au0 sd(:Au0) :WAT sd(:WAT)
-0.8750 0.000 0.00000 0.000 0.00000
If I plot it out it looks like the water density doesn't start until
about 30 Angstroms.
Also, I see you're using cpptraj version 15, which is several years
out of date. I highly recommend updating AmberTools and/or getting the
GitHub version of cpptraj.
Hope this helps,
-Dan
On Mon, Mar 25, 2019 at 1:42 PM Lucas Bandeira
<bandeiralucas97.gmail.com> wrote:
>
> Dear AMBER Community,
>
> I'm trying to compute density over z direction using the command "density".
> The system is a slab of gold with 12 layers under a water box. The result I
> got after computing density is a graph with 12 peaks, value which is equal
> the amount of layer that I have in the gold slab. But I can't understand
> the result I got. Why am I getting only the peaks related to the gold atoms
> and not the ones related to the water molecules. I can't understand the
> intensity of each peak neither. Could somebody help me?
>
> I'm sending attached the graphs I got and my input file to compute
> diffusion.
>
> Yours sincerely,
>
> Lucas Bandeira
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Received on Tue Mar 26 2019 - 12:30:02 PDT
