[gmx-users] gromacs.org_gmx-users Digest, Vol 181, Issue 45

[Nidhin Thomas]

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 fluctuation in the beginning but stabilized soon. The simulation continued without fail. 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
(1.322000)

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 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

Thanks,

Nidhin Thomas



> On 5/19/19 11:32 PM, Nidhin Thomas wrote:
>> Hello GROMACS users,
>> 
>> I tried to apply a static electric field across a water box. I used  anisotropic pressure coupling. Details of the pressure coupling is given below.
>> 
>> pcoupl                  = Parrinello-Rahman
>> pcoupltype              = anisotropic
>> tau_p                   = 5.0
>> compressibility         = 4.5e-5 4.5e-5 4.5e-5 0 0 0
>> ref_p                   = 1.0 1.0 1.0 0 0 0
>> ;
>> constraints             = h-bonds
>> constraint_algorithm    = LINCS
>> continuation            = yes
>> ;
>> electric-field-y = 0.1 0 0 0
>> 
>> I see that water box size reduced in the direction of application of electric field (Y) and increased in X and Z direction.
>> 
>> Original Size = (3.90 x 3.90 x 3.90) nm
>> Final Size     = (4.39 x 2.66 x 5.16) nm
>> 
>> Could someone please help me understand why the water box is shrinking in the direction of electric field ? can someone please let me know how external electric field is actually implemented in GROMACS ?
> 
> Anisotropic pressure coupling intrinsically leads to the distortion of 
> the box shape. Run a control simulation of water with no electric field 
> and you will see the same thing.
> 
> -Justin
> 
> -- 
> ==================================================
> 
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> 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
> http://www.thelemkullab.com
> 
> ==================================================