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