<span class="Apple-style-span" style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse; ">Date: Fri, 31 Dec 2010 19:08:50 -0500<br>From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu" style="color: rgb(0, 0, 204); ">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" style="color: rgb(0, 0, 204); ">gmx-users@gromacs.org</a>><br>Message-ID: <<a href="mailto:4D1E7092.7060309@vt.edu" style="color: rgb(0, 0, 204); ">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></span><div><span class="Apple-style-span" style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse; "><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 lot.<br>><br><br>> Possibly, but without seeing what you used for input, information about your<br>
> simulation, etc it's impossible to say.<br>In the electrons.dat file, I had </span></div><div><span class="Apple-style-span" style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse; ">2 </span></div>
<div><span class="Apple-style-span" style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse; ">OW = 8.834<br></span></div><div><span class="Apple-style-span" style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse; ">HW1 = 0.583</span></div>
<div><span class="Apple-style-span" style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse; ">HW2 = 0.583</span></div><div><span class="Apple-style-span" style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse; ">And then used g_density ... -ei electrons.dat -dens electron ...</span></div>
<div><span class="Apple-style-span" style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse; "><br></span></div><div><span class="Apple-style-span" style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse; "><br>
-Justin</span></div>