Re: [gmx-users] Calculating electron density profile of a lipid bilayer system
Thank you very much. I very much appreciate it.
Best wishes,
Azadeh
On Fri, May 31, 2019 at 12:24 PM ABEL Stephane 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 TIP3OH2 1 -0.83415.9994 ;
> 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
> 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
> 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
> > 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? Read http://www.gromacs.org/Support/Mailing_Lists
>
Re: [gmx-users] Calculating electron density profile of a lipid bilayer system
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 TIP3OH2 1 -0.83415.9994 ; 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
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: Re: [gmx-users] Calculating electron density profile of a
lipid bilayer system
Message-ID:
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 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
> 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? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
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Re: [gmx-users] Calculating electron density profile of a lipid bilayer system
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 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
> 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? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
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Re: [gmx-users] Calculating electron density profile of a lipid bilayer system
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
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Fwd: Calculating electron density profile of a
lipid bilayer system
Message-ID:
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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[gmx-users] Calculating electron density profile of a lipid bilayer system
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? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
