Re: Electric field simulation: eFieldNormalized

From: Giacomo Fiorin (
Date: Wed Nov 29 2017 - 08:48:05 CST

Hi Carlo, if you run NVT the statement about unit cell fluctuations and
virial contributions does not apply. eFieldNormalized does, however, use
the unit cell dimensions to define the units of the electric field so you
should leave the flag on even after you switch from NPT to NVT.

Please note also that eFieldNormalized does not protect you from "excessive
pressure": it simply defines the electric field with units relative to the
unit cell.


On Tue, Nov 28, 2017 at 2:53 PM, Carlo Guardiani <> wrote:

> Dear NAMD experts,
> I would like to run constant electric field
> simulations of an ion channel embedded in
> its membrane. At first I tried to run my
> simulation at constant pressure using the
> commands:
> eFieldOn yes
> eField 0.0 0.0 -0.134
> eFieldNormalized yes
> The simulation however, aborted immediately
> with the following error message:
> "FATAL ERROR: Periodic cell has become too
> small for original patch grid!
> Possible solutions are to restart from a
> recent checkpoint, increase margin, or
> disable useFlexibleCell for liquid
> simulation."
> I therefore tried to rerun the job at
> constant volume and the simulation
> could run without problems. However,
> I don't know what to do with the
> instruction
> eFieldNormalized yes
> As far as I understand, this statement
> is intended to avoid excessive pressure
> in an NPT simulation in the presence of
> a constant electric field. Do I have to
> keep this instruction also when running
> in the NVT ensemble ? And in such a case,
> which voltage would I be actually applying ?
> In the absence of scaling of the electric field
> the voltage should be computed as:
> V = Ez*Lz*43.17
> where V is the voltage in mV, Ez is the electric
> field in kcal/(mol*Ang*e), Lz is the dimension of
> the simulation box in Angstrom and 43.17 is the
> conversion factor.
> If the eField vector is scaled by the reciprocal
> lattice vectors at each timestep, the effective Ez
> is no longer the nominal one declared with the
> eField < electric field vector > instruction in the
> input file. Which formula should I use then to compute
> the effective potential I am applying ?
> Many thanks for your help and best wishes,
> Carlo Guardiani

Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Contractor, National Institutes of Health, Bethesda, MD

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