Thank you very much. I very much appreciate it. Best wishes, Azadeh
On Fri, May 31, 2019 at 12:24 PM ABEL Stephane <stephane.a...@cea.fr> wrote: > Hello > > >> Could you please give an example on how to modify the number of > electrons? Do I need to use the itp file? > As it is said in the gmx density -h > > "The first line contains the number of lines to read from the file. There > should be one line for each unique atom name in your system. The number of > electrons for each atom is modified by its atomic partial charge." > > So for instance, the CHARMM TIP3P atom have the following charges > (according the itp) > > 1 OT 1 TIP3 OH2 1 -0.834 15.9994 ; > qtot -0.834 > 2 HT 1 TIP3 H1 2 0.417 1.0080 ; > qtot -0.417 > 3 HT 1 TIP3 H2 3 0.417 1.0080 ; > qtot 0.000 > > So in your electron.dat you should have for water, > > 3 > OH2 = 7.166 ---> 8 -0.834 > H1 = 1.417 --> 1 + 0.417 > H2 = 1.417 --> 1 + 0.417 > > HTH > > > > ---------------------------------------------------------- > > > Message: 4 > Date: Fri, 31 May 2019 10:19:56 +0200 > From: Azadeh Alavizargar <azadeh.alavizar...@gmail.com> > To: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: Re: [gmx-users] Calculating electron density profile of a > lipid bilayer system > Message-ID: > < > calmoi-ag_gbaskku3yxtqrxrv5dvrsescg1ad4_mqjesfqa...@mail.gmail.com> > Content-Type: text/plain; charset="UTF-8" > > 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? 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