thanks mate! Igor Marques
On Thu, May 26, 2011 at 6:12 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Igor Marques wrote: > >> 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? >> >> > No. It is electrons/nm^3. Standard units are defined in Chapter 2 of the > manual (and printed in the code, of course). > > -Justin > > 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 <jianhuit...@gmail.com<mailto: >> jianhuit...@gmail.com>> 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" <jalem...@vt.edu <mailto:jalem...@vt.edu>> >> Subject: Re: [gmx-users] electron density >> To: Discussion list for GROMACS users <gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org>> >> Message-ID: <4d1f78ed.5070...@vt.edu <mailto:4d1f78ed.5070...@vt.edu>> >> >> >> 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" <jalem...@vt.edu >> <mailto:jalem...@vt.edu> <mailto:jalem...@vt.edu >> >> <mailto:jalem...@vt.edu>>> >> > Subject: Re: [gmx-users] electron density >> > To: Discussion list for GROMACS users <gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> > <mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>> >> >> > >> > Message-ID: <4d1e7092.7060...@vt.edu >> <mailto:4d1e7092.7060...@vt.edu> <mailto:4d1e7092.7060...@vt.edu >> >> <mailto:4d1e7092.7060...@vt.edu>>> >> > 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 gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> 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 gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>. >> >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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