Re: [gmx-users] External electric field applied to water box

[Alex]

Oops. Yes, we most certainly have a semiisotropic setup. I think I misread
the original message. Well, this is why I don't post much lately.
:-)

Alex

On Wed, May 22, 2019, 11:39 AM Justin Lemkul  wrote:

>
>
> On 5/22/19 1:34 PM, Alex wrote:
> > 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.
> >
>
> That's a very different system than a box of pure water. If your XY size
> is fixed (essentially NPAT), is anistropic coupling even relevant or
> necessary? Membranes are classic semiisotropic systems, which you have
> by fixing the XY vectors, no?
>
> I'm mostly curious about the setup. I used anisotropic coupling a long
> time for membranes and routinely observed square cross-sections become
> rectangular over 100 ns or so (not a big deal but still not really
> physically relevant) and I never see anyone doing membrane systems
> deviate from semiisotropic coupling, because it's the most intuitive.
>
> -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
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==
>
> --
> Gromacs Users mailing list
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Re: [gmx-users] External electric field applied to water box

[Justin Lemkul]

On 5/22/19 1:34 PM, Alex wrote:
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.




That's a very different system than a box of pure water. If your XY size 
is fixed (essentially NPAT), is anistropic coupling even relevant or 
necessary? Membranes are classic semiisotropic systems, which you have 
by fixing the XY vectors, no?


I'm mostly curious about the setup. I used anisotropic coupling a long 
time for membranes and routinely observed square cross-sections become 
rectangular over 100 ns or so (not a big deal but still not really 
physically relevant) and I never see anyone doing membrane systems 
deviate from semiisotropic coupling, because it's the most intuitive.


-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

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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Re: [gmx-users] External electric field applied to water box

[Alex]

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.


Alex


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 
(1.00) 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 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 
 



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


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Re: [gmx-users] External electric field applied to water box

[Justin Lemkul]

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 (1.00) 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 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
 



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

--
==

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

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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[gmx-users] External electric field applied to water box

[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 
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 (1.00) 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 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
 


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
> 
> jalem...@vt.edu  | (540) 231-3129
> http://www.thelemkullab.com 
> 
> ==
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Re: [gmx-users] External electric field applied to water box

[Justin Lemkul]

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

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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[gmx-users] External electric field applied to water box

[Nidhin Thomas]

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 ?

Thanks a lot for your help!.

Nidhin Thomas
University of Houston
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