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

[Azadeh Alavizargar]

Thank you very much. I very much appreciate it.

Best wishes,
Azadeh

On Fri, May 31, 2019 at 12:24 PM ABEL Stephane <Stephane.ABEL at 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.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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