Problem solved. The "2" in the text is just a typo when I sent the email. So actually there is no partial charge in the electrons.dat file. Thanks, Justin.
Jianhui Date: Sat, 01 Jan 2011 13:56:45 -0500 From: "Justin A. Lemkul" <[email protected]> Subject: Re: [gmx-users] electron density To: Discussion list for GROMACS users <[email protected]> Message-ID: <[email protected]> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Jianhui Tian wrote: > Date: Fri, 31 Dec 2010 19:08:50 -0500 > From: "Justin A. Lemkul" <[email protected] <mailto:[email protected]>> > Subject: Re: [gmx-users] electron density > To: Discussion list for GROMACS users <[email protected] > <mailto:[email protected]> > > Message-ID: <[email protected] <mailto:[email protected]>> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > 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
-- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
