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 <[email protected]
<mailto:[email protected]>> 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" <[email protected] <mailto:[email protected]>>
Subject: Re: [gmx-users] electron density
To: Discussion list for GROMACS users <[email protected]
<mailto:[email protected]>>
Message-ID: <[email protected] <mailto:[email protected]>>
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Jianhui Tian wrote:
> Date: Fri, 31 Dec 2010 19:08:50 -0500
> From: "Justin A. Lemkul" <[email protected]
<mailto:[email protected]> <mailto:[email protected]
<mailto:[email protected]>>>
> Subject: Re: [gmx-users] electron density
> To: Discussion list for GROMACS users <[email protected]
<mailto:[email protected]>
> <mailto:[email protected] <mailto:[email protected]>>
>
> Message-ID: <[email protected]
<mailto:[email protected]> <mailto:[email protected]
<mailto:[email protected]>>>
> 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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