[gmx-users] electron density

[Igor Marques]

dear all,

regarding the matter of electron density, can anyone clarify me on the
output units?
from this discussion i understand the values are presented in electrons/A^3
- is this correct?

best regards,
igor


Igor Marques

Molecular Modeling Group – Univ. of Aveiro
http://molecular-modeling.dq.ua.pt/



On Sat, Jan 1, 2011 at 9:01 PM, Jianhui Tian <jianhuitian at gmail.com> wrote:

> Problem solved.
> The "2" in the text is just a typo when I sent the email.
> So actually there is no partial charge in the electrons.dat file.
> Thanks, Justin.
>
> Jianhui
>
> Date: Sat, 01 Jan 2011 13:56:45 -0500
>
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] electron density
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4D1F78ED.5070302 at vt.edu>
>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> Jianhui Tian wrote:
> > Date: Fri, 31 Dec 2010 19:08:50 -0500
> > From: "Justin A. Lemkul" <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
> > Subject: Re: [gmx-users] electron density
> > To: Discussion list for GROMACS users <gmx-users at gromacs.org
> > <mailto:gmx-users at gromacs.org>
> >
> > Message-ID: <4D1E7092.7060309 at vt.edu <mailto:4D1E7092.7060309 at vt.edu>>
> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> >
> >
> >
> > Jianhui Tian wrote:
> >>  Hi gmx users,
> >>
> >>  I tried to calculate both the mass density and electron density for the
> >>  water layer of a membrane simulation. The mass density is 1000 kg/m^3,
> >>  however the electron density I got is smaller than about 0.33 e/A^3. I
> >
> >>  How much smaller?
> > I got about 0.27 e/A^3.
> >
> >>  am using a CHARMM force field and the CHARMM version of TIP3P water. Am
> >>  I doing anything wrong when calculating the electron density? Thanks a
> > lot.
> >>
> >
> >>  Possibly, but without seeing what you used for input, information
> > about your
> >>  simulation, etc it's impossible to say.
> > In the electrons.dat file, I had
> > 2
> > OW = 8.834
> > HW1 = 0.583
> > HW2 = 0.583
> > And then used g_density ... -ei electrons.dat -dens electron ...
> >
>
> There are several problems.  The first line of electrons.dat indicates
> there are
> only two unique atom names, but clearly you're supplying three.  Second,
> this
> file is read in such that at integral number of electrons is detected on
> each
> line.  So, in your case, two lines are being read, one that detects 8
> electrons,
> and another that detects zero.
>
> -Justin
>
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