[gmx-users] External electric field applied to water box
nedomacho at gmail.com
Wed May 22 19:34:56 CEST 2019
To quickly chime in: we routinely use anisotropic coupling for
relaxation (constant box size in XY) without any issues. There is a good
reason for that in our case (an XY-membrane splitting the box mid-Z,
which we don't want to mangle). Again, no issues whatsoever. Water is
TIP4P in our case. I suspect issues with setup in your case.
On 5/22/2019 11:17 AM, Justin Lemkul wrote:
> 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?
> 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.
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