Re: eFieldNormalized

From: Fateme Ghadirian (
Date: Sun Dec 05 2021 - 09:29:36 CST


May be I did not properly describemy problem.

This is the issue’s details:

Iwanted to add a constant electric field (not constant potential drop betweenthe edges of the system) on my fully hydrated bilayer in NPT ensemble simulation.I saw there was ‘eFieldNormalized’ keyword and I did not get what exactly itdoes, even by searching and studying some related links (even though it seemed to me that it maybe somehow affects system’s pressure, but in the second link of previous email,it has mentioned that when eFieldNormalized is true the eField forces do notcontribute to the pressure calculation).

So Ihave ran 2 identical fully hydrated bilayer systems, with and without eFieldNormalizedkeyword.

For bothof them the electric fields has been applied in z direction (bilayer’s normal)and its value was chosen a big one ( Ez (kcal/mol.A.e)*Lz(A)*0.0434(Volts/A)=10Volts,Box_Lz~100 Ang ) to see the visual differences. Periodic boundary conditionswere applied in all directions.

WitheFieldNormalized set to on, I could not see any pore formation in the lipidbilayer, or even any water fingers in the hydrophobic part of bilayer. It seemsif I want to see pore formation, eFieldNormalized musb be off?!

And bychecking Total energy and volume of the system (when eFieldNormalized set to on),there were not any changes before and after exerting the electric field! Butfor the case without eFieldNormalized (efield on, eFieldNormalized off), therewas a great drop in Total energy and Volume of the system right after exertingthe e field and then with time passing, they stood steady. And also there waspore formation and even lipid distortion.

Whythere is no change in total energy and volume of the system wheneFieldNormalized set to on? and why there is no pore formation, even with sucha big electric field value?! Is it because when eFieldNormalized is true the eField forces do not contribute to thepressure calculation?

Byprevious email, I meant eFieldNormalized exact function, which I am trying toget by different simulations.

Alsothe contents of link that you have mentioned, seems the same as the link that Isent before, to me. I did not see any differences or updates. There was thesame description of eFieldNormalized in both of them.



    On Sunday, December 5, 2021, 12:12:34 AM GMT+3:30, Giacomo Fiorin <> wrote:
 Part of the info that you're asking to clarify is not correct.
The second of the two links that you shared is the documentation of the electric keywords, i.e. it is not a tutorial with a pre-cooked input that you may copy and paste for your pruse.  Here's the updated one for 2.14:
Just because the eFieldNormalized keyword is listed in the manual, it doesn't mean that you must necessarily add it to your input.  It is there for you to read what that keyword does, and then decide whether it's needed based on the specifics of your scientific question.

Do you want to specify a constant field, or a constant potential drop between the edges of the unit cell?  That's essentially what that keyword is asking.  That decision is up to you.


On Sat, Dec 4, 2021 at 9:00 AM Fateme Ghadirian <> wrote:

Dear NAMD users,
I have a system which contains a fully hydrated bilayer with some particles in the aqueous part of the system. I did not use any free ions in the aqueous part of the system, so I justhave water +Bilayer + water+ some neutral particles in water.  The simulation run is in NPT to represent atmospheric pressure of a natural cell. I want to addconstant electric field in the z direction (bilayer's normal vector) to this system to investigate its possible effects on theparticles and the bilayer. In the following tutorial:

It has used

eFieldOn yes

eField 0.0 0.0 -0.134
In its .conf file to run the constant electric field simulation.

But in the following link

The electric field in the .conf file has been applied as follows

eFieldOn yes

eField 0.0 0.0 -0.134

eFieldNormalized yes

By searching in namd-l threads, I have found some opposite explanations about eFieldNormilized, which are given below:
namd-l: Re: Electric field simulation: eFieldNormalized

| |
namd-l: Re: Electric field simulation: eFieldNormalized




1) The eFieldNormilized statement is intended to avoid excessive pressure in an NPT simulation in the presence of a constant electric field.

2) The eFieldNormalized does not protect the simulation from “excessive pressure”: it simply defines the electric field with units relative to the unit cell.

I do not understand what eFieldNormalized means and what its function in an electric field simulation is, any help for its clarification would be appreciated.
And also I need to apply constant electric field to my NPT simulation, should I use eFieldNormalized yes or not??? I do not have free ions in my system.
What are the consequences of not using the eFieldNormalized in Simulations?


Thanks in advance


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