# Re: [AMBER] cpptraj density command

From: Ignacio J. General <ijgeneral.gmail.com>
Date: Sun, 22 Nov 2015 11:09:41 -0300

Dear David and Dan, thanks so much for your replies. But I still have some
doubts about it, so let me be specific:

I am using the cpptraj command:

density out charge_density_nopep.dat charge delta 0.1 ":Cl-,:K+,:WAT,:1-385"

in order to calculate the charge density. It outputs a file containing
lines like this one:

25.6500 -0.610 3.68050

I believe the 1st column is z, 2nd charge density and, is the 3rd one
standard deviation (as it says "sd", although I am not sure what statistics
it is doing...)?

I am trying to solve Poisson's equation, where on the right hand side I
have rho, the charge density (say in units of C/A^3). So my specific
question is: how do I convert that -0.610 in the output file to C/A^3?

Is it just dividing by the area of the box, x*y, and multypling by the
charge of the electron?

I know I can test this by looking at the order of magnitude, but I have
written a program to do this, and I am getting a wrong order of magnitude,
so I am not sure at this point if my error is in the code or in my
interpretation of the cpptraj numbers, or in both...

Ignacio

On Sat, Nov 21, 2015 at 2:59 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:

> FYI, there is also this entry in the Amber15 manual for the 'density'
> command:
>
> "number|mass|charge|electron Number, mass, partial charge (q) or
> electron (Ne - q)
> density. To convert the electron density to e-/Å3 divide by the (average)
> area spanned by the other two dimensions. (number)"
>
> -Dan
>
> On Sat, Nov 21, 2015 at 6:54 AM, David A Case <david.case.rutgers.edu>
> wrote:
> > On Sat, Nov 21, 2015, Ignacio J. General wrote:
> >>
> >> density out density.dat charge 0.1 ":1-451"
> >>
> >> in units of Coulomb / A^3? Or is in units of electron charge / A^3?
> >
> > Amber never uses Coulombs, which in any event would be 19 orders of
> magnitude
> > different than the electron charge, so pretty easy to spot.
> >
> > Amber uses charges in electron charge and distances in Ang., so a charge
> > density should be in units of e/A^3. There are various ways to check
> this,
> > e.g. just take a single ion, compute the charge density on a grid, and
> sum up
> > all of the values.
> >
> >> PD: I sent this message yesterday, but didn't appear in the mail
> archive,
> >> so I am sending it again. Sorry if, after all, it gets there 2 times...
> >
> > The archive is only updated a few times a week, so there can be a time
> lag
> > before items appear.
> >
> > ....dac
> >
> >
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
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Received on Sun Nov 22 2015 - 06:30:04 PST
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