dear all,<div><br></div><div>regarding the matter of electron density, can anyone clarify me on the output units?</div><div>from this discussion i understand the values are presented in electrons/A^3 - is this correct?</div>
<div><br></div><div>best regards,</div><div>igor</div><div><br></div><div><br></div><div><span style="COLOR: gray; mso-bidi-font-family: calibri; mso-bidi-theme-font: minor-latin; mso-themecolor: background1; mso-themeshade: 128; mso-ansi-language: en-us" lang="EN-US">Igor Marques</span></div>
<div><span style="COLOR: gray; mso-bidi-font-family: calibri; mso-bidi-theme-font: minor-latin; mso-themecolor: background1; mso-themeshade: 128; mso-ansi-language: en-us" lang="EN-US"><br></span></div><div><span style="COLOR: gray; mso-bidi-font-family: calibri; mso-bidi-theme-font: minor-latin; mso-themecolor: background1; mso-themeshade: 128; mso-ansi-language: en-us" lang="EN-US">Molecular Modeling Group – Univ. of Aveiro<br>
<a href="http://molecular-modeling.dq.ua.pt/">http://molecular-modeling.dq.ua.pt/</a></span></div><div><br>
<br><br><div class="gmail_quote">On Sat, Jan 1, 2011 at 9:01 PM, Jianhui Tian <span dir="ltr"><<a href="mailto:jianhuitian@gmail.com">jianhuitian@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
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<div class="im">
<br>
From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>><br></div><div class="im">
Subject: Re: [gmx-users] electron density<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br></div>
Message-ID: <<a href="mailto:4D1F78ED.5070302@vt.edu" target="_blank">4D1F78ED.5070302@vt.edu</a>><div><div></div><div class="h5"><br>
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<br>
<br>
<br>
Jianhui Tian wrote:<br>
> Date: Fri, 31 Dec 2010 19:08:50 -0500<br>
> From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">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" target="_blank">gmx-users@gromacs.org</a><br>
> <mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><div>><br>
> Message-ID: <<a href="mailto:4D1E7092.7060309@vt.edu" target="_blank">4D1E7092.7060309@vt.edu</a> <mailto:<a href="mailto:4D1E7092.7060309@vt.edu" target="_blank">4D1E7092.7060309@vt.edu</a>>><br>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
><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>
</div>
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