From: Fateme Ghadirian (fateme.ghadirian_at_yahoo.com)
Date: Sat Nov 20 2021 - 10:26:31 CST
Dear NAMD users,
I have a system which contains afully hydrated bilayer with some particles in the aqueous part of the system. Thesimulation run is in NPT. I want to add constant electricfield to this system to investigate its possible effects on the particles andthe 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 do 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 hasapplied as follows
eFieldOn yes
eField 0.0 0.0 -0.134
eFieldNormalized yes
By searching in namd-l questions, I foundsome opposite explanations about eFieldNormilized:
https://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2016-2017/2486.html
1) The eFieldNormilized statement is intended toavoid excessive pressure in an NPTsimulation in the presence of a constant electric field.
2) The eFieldNormalized does not protect the simulation from “excessivepressure”: it simply defines the electric field with units relative to the unitcell.
I do not understand what eFieldNormalizedmeans and what its function in an NPT simulation is, any help for itsclarification would be appreciated.
And also I need to apply constant electricfield to my NPT simulation, should I use eFieldNormalized yes or not???
What are the consequences of not using theeFieldNormalized in Simulations?
Thanks in advance
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