[gmx-users] electron density

[Justin A. Lemkul]

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>>
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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

> 
> -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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