Hello Azadeh 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: 1 Date: Sat, 25 May 2019 13:21:32 +0200 From: Azadeh Alavizargar <azadeh.alavizar...@gmail.com> To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] Calculating electron density profile of a lipid bilayer system Message-ID: <CALMOi-ZCGboBM411sjoOO+CnOqZoOpLwmJ4_so=gokhhf1a...@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.