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

From: Gargi Borgohain <gargib2011.gmail.com>
Date: Fri, 17 May 2019 15:15:31 +0530

Thank you for your reply.
I have attached herewith the whole md.out file. The average and rms
fluctuation steps are as such

      A V E R A G E S O V E R 20 S T E P S


 NSTEP = 20000 TIME(PS) = 580.000 TEMP(K) = 302.32 PRESS =
0.0
 Etot = -81753.2804 EKtot = 16352.4793 EPtot =
-98105.7597
 BOND = 510.1009 ANGLE = 1415.7121 DIHED =
2186.3520
 1-4 NB = 564.0489 1-4 EEL = 8317.5640 VDWAALS =
9687.9893
 EELEC = -104009.8605 EHBOND = 0.0000 RESTRAINT =
0.0000
 ELECTRIC_FIELD = -16777.6663
 Ewald error estimate: 0.1321E-03
 ------------------------------------------------------------------------------


      R M S F L U C T U A T I O N S


 NSTEP = 20000 TIME(PS) = 580.000 TEMP(K) = 7.84 PRESS =
0.0
 Etot = 1801.5803 EKtot = 424.0761 EPtot =
1413.5228
 BOND = 19.6490 ANGLE = 31.0534 DIHED =
21.7425
 1-4 NB = 13.0859 1-4 EEL = 35.2505 VDWAALS =
229.2162
 EELEC = 967.6214 EHBOND = 0.0000 RESTRAINT =
0.0000
 ELECTRIC_FIELD = 759.1694
 Ewald error estimate: 0.6740E-04
 ------------------------------------------------------------------------------
Further, I would like to mention that electric field of 300 V/m causes
denaturation of the protein as simulation begins. But most of the
simulations (in literature) uses electric field of 3.0 V/nm or 3000000 V/m.
When I use efz=3000000 then simulation is killed itself with following
comments:

vlimit exceeded for step 0; vmax = 848.0847
Coordinate resetting cannot be accomplished,
deviation is too large
iter_cnt, my_bond_idx, i and j are : 1 20 28 30

Can you please help me out how to set up electric field at 3 V/nm
accurately?
Thanks.
Regards
Gargi

Date: Thu, 16 May 2019 15:06:50 +0000
From: Charles Lin <Charles.lin.silicontx.com>
Subject: Re: [AMBER] ELECTRIC_FIELD in md.out file does not match with
        md.in file
To: AMBER Mailing List <amber.ambermd.org>
Message-ID: <89FD94CD-FE25-4B5D-8E55-BD201BA59BF7.silicontx.com>
Content-Type: text/plain; charset="utf-8"

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


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Received on Fri May 17 2019 - 03:00:02 PDT
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