# Re: [AMBER] Problems calculating density over distance

From: Lucas Bandeira <bandeiralucas97.gmail.com>
Date: Mon, 1 Apr 2019 13:13:25 -0300

OK. Thank you Daniel. It helped me a lot.

I can see the density for water molecules now, but I have one more
question, Why cannot I see the peaks related to the water molecules, could
you help me with this?

Yours sincerely,

Lucas Bandeira

On Tue, Mar 26, 2019 at 4:08 PM Daniel Roe <daniel.r.roe.gmail.com> wrote:

> 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 out of date.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 Mon Apr 01 2019 - 09:30:02 PDT
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