From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Sat Dec 04 2021 - 14:09:38 CST
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:
https://www.ks.uiuc.edu/Research/namd/2.14/ug/node42.html
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.
Giacomo
On Sat, Dec 4, 2021 at 9:00 AM Fateme Ghadirian <
fateme.ghadirian_at_remove_yahoo.com> 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 just have 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 add constant
> electric field in the z direction (bilayer's normal vector) to this
> system to investigate its possible effects on the particles and the
> bilayer. In the following tutorial:
>
>
> http://bionano.physics.illinois.edu/tutorials/electrostatic-maps-and-ion-conduction
>
> 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*
>
> https://www.ks.uiuc.edu/Research/namd/2.10b1/ug/node42.html
>
> *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
> <https://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2016-2017/2486.html>*
>
> *namd-l: Re: Electric field simulation: eFieldNormalized
> <https://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2016-2017/2486.html>*
>
>
> *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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