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

[ABEL Stephane]

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.alavizargar at gmail.com>
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: Re: [gmx-users] Calculating electron density profile of a
        lipid bilayer system
Message-ID:
        <CALMOi-ag_gBASkku3YXTqRxrV5dvrsEsCG1ad4_MqjEsFQAeDg at 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.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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