Hi Gargi,
As far as I understand it seems a problem of unit conversions. If
I'm not wrong, 1 V/nm is about 2.3060 kcal/(mol A e)
Then 3 V/nm should be set as efz=6.918
Joan
El 17/5/19 a les 11:45, Gargi Borgohain ha escrit:
> 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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--
Joan Torras-Costa
Department of Chemical Engineering
Universitat Politècnica de Catalunya
Escola d'Enginyeria de Barcelona Est (EEBE)
Campus Diagonal Besòs, Building I
C. Eduard Maristany, 10-14 08019 Barcelona
SPAIN
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Received on Fri May 17 2019 - 04:00:02 PDT
