[gmx-users] Calculating electron density profile of a lipid bilayer system

[Azadeh Alavizargar]

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.ABEL at 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.alavizargar at gmail.com>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] Fwd: Calculating electron density profile of a
>         lipid   bilayer system
> Message-ID:
>         <
> CALMOi-YG2beR7V1XPwMPsAwsoY+BPtW1y88Or3zf++BOwoaUeA at 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]
>
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