[gmx-users] electron density

[Justin A. Lemkul]

Igor Marques wrote:
> 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?
> 

No.  It is electrons/nm^3.  Standard units are defined in Chapter 2 of the 
manual (and printed in the code, of course).

-Justin

> 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 
> <mailto: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 <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: <4D1F78ED.5070302 at vt.edu <mailto:4D1F78ED.5070302 at vt.edu>>
> 
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> 
> 
> 
>     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> <mailto: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>
>      > <mailto:gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>
>      >
>      > Message-ID: <4D1E7092.7060309 at vt.edu
>     <mailto:4D1E7092.7060309 at vt.edu> <mailto:4D1E7092.7060309 at vt.edu
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>      >
>      >
>      >
>      > 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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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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