[gmx-users] electron density

[Igor Marques]

thanks mate!

      Igor Marques


On Thu, May 26, 2011 at 6:12 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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>>
>>
>>
>>    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> <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
>>
>>    <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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>>
> --
> ========================================
>
> 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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