[gmx-users] External electric field applied to water box
jalemkul at vt.edu
Wed May 22 19:17:12 CEST 2019
On 5/22/19 9:03 AM, Nidhin Thomas wrote:
> Dear Justin,
> Thanks a lot for the prompt reply.
> I ran another simulation with a larger box size with and without external electric field (field direction is Y-axis). I used anisotropic pressure coupling for both simulations. Water box without external electric field had stable system in the beginning but failed after couple of nano seconds. However, the system with external electric field deformed continuously. System with EF fails once the dimension of the box vector (Y-axis) along the direction of electric field reduces below the minimum box dimension. The error message is copied below.
> Fatal error:
> The Y-size of the box (2.641246) times the triclinic skew factor (1.000000) is
> smaller than the number of DD cells (2) times the smallest allowed cell size
> I feel that box is shrinking in the direction of applied electric field (Y-axis) like there is an external compressive stress applied in that direction. I do not understand how this type of a stress is generated in the system. I also tried the system with semiisotropic pressure coupling and the box deformed in Z direction and failed. When I used isotropic coupling, the system did not fail.
> I have also shared link to an image that shows how the box vectors are changing with simulation time. When EF is applied, simulation fails in few picoseconds. But water box without EF did not fail.
> Could you please help me understand why system with external electric field would behave different from water box without EF?
> https://www.dropbox.com/s/zu7vl2wr99sube2/Box%20vectors%20with%20and%20without%20EF.png?dl=0 <https://www.dropbox.com/s/zu7vl2wr99sube2/Box%20vectors%20with%20and%20without%20EF.png?dl=0>
I don't know if anyone has ever tested electric fields with anisotropic
coupling, but if a system of pure water with no external influence fails
with anisotropic coupling, I'd say that is an argument for not using
that type of coupling. There is no physical reason why a box of pure
water should be treated anisotropically - it is an isotropic medium, and
all water ever "sees" via PBC is water. So the box deformation is not
physically real or relevant.
Justin A. Lemkul, Ph.D.
Office: 301 Fralin Hall
Lab: 303 Engel Hall
Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
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