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

ABEL Stephane Stephane.ABEL at cea.fr
Thu May 30 14:49:38 CEST 2019


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.



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
        <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:
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,
[image: image.png]


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