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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
This email message is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. If you are the intended recipient, please be advised that the content of this message is subject to access, review and disclosure by the sender's Email System Administrator.
This email message is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. If you are the intended recipient, please be advised that the content of this message is subject to access, review and disclosure by the sender's Email System Administrator.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu May 16 2019 - 08:30:03 PDT
