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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...

Thanks again for your help!

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
*

*> >
*

*> >
*

*> > _______________________________________________
*

*> > AMBER mailing list
*

*> > 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)
*

*>
*

*> _______________________________________________
*

*> AMBER mailing list
*

*> AMBER.ambermd.org
*

*> http://lists.ambermd.org/mailman/listinfo/amber
*

*>
*

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Received on Sun Nov 22 2015 - 06:30:04 PST

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...

Thanks again for your help!

Ignacio

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

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

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Received on Sun Nov 22 2015 - 06:30:04 PST

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