dear all, regarding the matter of electron density, can anyone clarify me on the output units? from this discussion i understand the values are presented in electrons/A^3 - is this correct?
best regards, igor Igor Marques Molecular Modeling Group – Univ. of Aveiro http://molecular-modeling.dq.ua.pt/ On Sat, Jan 1, 2011 at 9:01 PM, Jianhui Tian <[email protected]> wrote: > 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 >
-- 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
