Dear Stephane Thank you very much for your reply. I am sorry, I had not noticed you have answered before and was thinking my message has not been sent so I sent it again. I am sorry, but I did not get you completely. How should I take into account the number of electrons? I thought that I just need to give the atomic number of each element in the electron.dat file. Could you please give an example on how to modify the number of electrons? Do I need to use the itp file?
Thanks a lot. Best regards, Azadeh On Thu, May 30, 2019 at 2:50 PM ABEL Stephane <stephane.a...@cea.fr> wrote: > Hello > > I gave you a response few days ago > > For the calculations of the EDP you have to take into account of the > charges of the atom (it is mentioned at the end of density tool ("known > issue")) . So modify the number of electrons to have the "real" electron > numbers in you electron.dat file accordingly. > > HTH > > ------------------------------ > > Message: 2 > Date: Thu, 30 May 2019 09:55:18 +0200 > From: Azadeh Alavizargar <azadeh.alavizar...@gmail.com> > To: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: [gmx-users] Fwd: Calculating electron density profile of a > lipid bilayer system > Message-ID: > < > calmoi-yg2ber7v1xpwmpsawsoy+bptw1y88or3zf++bowoa...@mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Dear Gromacs users > > I am trying to calculate the electron density profiles of a lipid bilayer > system. However I am not getting the correct profile. I would appreciate it > a lot if you can help me. > > Following is the procedure I go through: > > 1- first I create a ndx file to select the resnames: > > gmx select -f trj_file.trr -s tpr_file.tpr -on index_file.ndx -select > '(resname DPPC TIP3)' > > 2- Then I created the electron.dat file including all the atoms (including > hydrogens) of the selected atoms. The first lines look like this: > 208 > OH = 8 > H1 = 1 > H2 = 1 > N = 7 > C13 = 6 > H13A = 1 > H13B = 1 > H13C = 1 > C14 = 6 > H14A = 1 > H14B = 1 > H14C = 1 > C15 = 6 > ... > > 3- Then I use gmx density in order to calculate the electron density of the > selected resnames: > > gmx density -f trj_file.trr -s tpr_file.tpr -n index_file.ndx -o > density_traj_center.xvg -dens electron -ei electron.dat -center -relative > > However, what I get is not similar to the ones in papers: > Best regards, > Azadeh > [image: image.png] > > ------ > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.