Dear AMBER users
I am trying to do NVT simulation of a protein using static external
electric field in z-direction. I am using pmemd module of AMBER18 package
that supports use of external electric field. md.in file used is as such:
Production simulation NVT ensemble
&cntrl
imin = 0,
irest = 1,
ntx = 5,
ntb = 1,
cut = 9.0,
ntr = 0,
ntc = 2,
ntf = 2,
tempi = 300.0,
temp0 = 300.0,
ntt = 3,
gamma_ln = 1.0,
ig = -1,
iwrap = 1,
efx = 0,
efy = 0,
efz = 300,
efn = 1,
nstlim = 20000,
dt = 0.002,
ntpr = 1000, ntwx = 2000, ntwr = 2000
/
&ewald
nfft1=64, nfft2=64, nfft3=64,
/
The out file shows that ELECTRIC_FIELD = -16777.6663. As written in Amber18
reference manual efz sets z-component of the electric field in
kcal/(mol*A*e) or V/m. My questions are
(1) if efz sets electric field at 300 V/m then how md.out file shows
ELECTRIC_FIELD = -16777.6663 (averaged over 20000 steps)?
(2) Is the unit of electric field in md.out file modified?
(3) Is the magnitude of electric field in md.out file modified?
(4) How can I invoke expected electric field such as 3.0 V/nm in md.in file?
Looking forward for your kind explanations and suggestions.
Thanking you.
Dr. Gargi Borgohain
Department of Chemistry
Cotton University
Guwahati-781001. Assam. India
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Received on Thu May 16 2019 - 03:00:01 PDT
