thanks mate!<div><br clear="all"> Igor Marques<br>
<br><br><div class="gmail_quote">On Thu, May 26, 2011 at 6:12 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div class="im"><br>
<br>
Igor Marques wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
dear all,<br>
<br>
regarding the matter of electron density, can anyone clarify me on the output units?<br>
from this discussion i understand the values are presented in electrons/A^3 - is this correct?<br>
<br>
</blockquote>
<br></div>
No. It is electrons/nm^3. Standard units are defined in Chapter 2 of the manual (and printed in the code, of course).<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="im">
best regards,<br>
igor<br>
<br>
<br>
Igor Marques<br>
<br>
Molecular Modeling Group – Univ. of Aveiro<br>
<a href="http://molecular-modeling.dq.ua.pt/" target="_blank">http://molecular-modeling.dq.ua.pt/</a><br>
<br>
<br>
<br></div><div class="im">
On Sat, Jan 1, 2011 at 9:01 PM, Jianhui Tian <<a href="mailto:jianhuitian@gmail.com" target="_blank">jianhuitian@gmail.com</a> <mailto:<a href="mailto:jianhuitian@gmail.com" target="_blank">jianhuitian@gmail.com</a>>> wrote:<br>
<br>
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. Thanks, Justin.<br>
<br>
Jianhui<br>
<br>
Date: Sat, 01 Jan 2011 13:56:45 -0500<br>
<br></div><div class="im">
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>>><br></div>
Message-ID: <<a href="mailto:4D1F78ED.5070302@vt.edu" target="_blank">4D1F78ED.5070302@vt.edu</a> <mailto:<a href="mailto:4D1F78ED.5070302@vt.edu" target="_blank">4D1F78ED.5070302@vt.edu</a>>><div class="im">
<br>
<br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<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><br></div>
<mailto:<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><div class="im"><br>
<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>><br></div>
> <mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a> <mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>>><div class="im"><br>
><br>
> Message-ID: <<a href="mailto:4D1E7092.7060309@vt.edu" target="_blank">4D1E7092.7060309@vt.edu</a><br></div>
<mailto:<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><div><div></div><div class="h5">
<br>
<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<br>
for the<br>
>> water layer of a membrane simulation. The mass density is 1000<br>
kg/m^3,<br>
>> however the electron density I got is smaller than about 0.33<br>
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<br>
water. Am<br>
>> I doing anything wrong when calculating the electron density?<br>
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<br>
indicates there are<br>
only two unique atom names, but clearly you're supplying three.<br>
Second, this<br>
file is read in such that at integral number of electrons is<br>
detected on each<br>
line. So, in your case, two lines are being read, one that detects<br>
8 electrons,<br>
and another that detects zero.<br>
<br>
-Justin<br>
<br>
--<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br></div></div><div class="im">
<mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br></div><div class="im">
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at<br>
<a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the<br>
www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a><br></div>
<mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>>.<div class="im"><br>
Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
<br>
<br>
</div></blockquote><div class="im">
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
-- <br></div><div><div></div><div class="h5">
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
</div></div></blockquote></div><br></div>