Re: [AMBER] ELECTRIC_FIELD in md.out file does not match with md.in file

From: Charles Lin <Charles.lin.silicontx.com>
Date: Thu, 16 May 2019 15:06:50 +0000

AMBER outputs energies in kcal/mol. The electric field you chose invokes around 300 V/m per atom in the z-direction. Essentially the forces are based on charge of atom * electric field, and energies are calculated along the lines of the force * (box offset).

Hope that helps,
Charlie

´╗┐On 5/16/19, 6:04 AM, "Bill Ross" <ross.cgl.ucsf.edu> wrote:

    I don't know the answer, but it will likely help if you paste the whole
    section of numbers for the step and/or summary.

    Bill

    https://www.reddit.com/r/learnmachinelearning/comments/bnzhtr/drilling_into_the_mind_with_ducttapey_nets_and_a/


    On 5/16/19 2:38 AM, Gargi Borgohain wrote:
> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber

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Received on Thu May 16 2019 - 08:30:03 PDT
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