[gmx-users] p-coupling for inverted hexagonal phase

[Mohsen Ramezanpour]

Thanks Justin for your comment,

I think applying the semi-isotropic will put too much symmetry on the
system while it might not be the case and system should be free to change
if it is energetically favourable.
The semi-isotropic, in fact, is scaling both the X and Y sides of the
simulation box with the same factor, if I understood correctly. So, it will
keep the original geometry of the system the same through the simulation
time.
Think of situations where the water channels prefer to be elongated in
either X or Y direction. This will prevent this, right?
Also, if there is any phase transition possible (e.g. from HII to
Lamellar), semi-isotropic will probably limit this transition more than
what an anisotropic coupling will do.

Please let me know your thoughts on this.

Cheers,
Mohsen


On Wed, Sep 27, 2017 at 6:26 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 9/27/17 10:57 AM, Mohsen Ramezanpour wrote:
>
>> Hi Everyone,
>>
>> Please let me know your thoughts on this.
>>
>>
> I don't see why these would be anisotropic. The lateral dimension is
> symmetric, so it seems that semiisotropic would be most appropriate.
> Anisotropic pressure coupling can lead to significant distortions of the
> box, and is most applicable in crystalline systems.
>
> -Justin
>
> Thanks in advance,
>> Cheers,
>> Mohsen
>>
>> On Fri, Sep 22, 2017 at 11:13 AM, Mohsen Ramezanpour <
>> ramezanpour.mohsen at gmail.com> wrote:
>>
>> Dear Gromacs users,
>>>
>>> I am doing a simulation on inverted hexagonal (HII) phase composed of
>>> just
>>> lipids and water.
>>>
>>> (please have a look at HII phase here:
>>> https://openi.nlm.nih.gov/detailedresult.php?img=
>>> PMC2695813_1757-5036-2-3-3&req=4)
>>>
>>> My question is regarding the pressure coupling for such systems. I am
>>> using the anisotropic p-coupling at the moment:
>>>
>>> pcoupl                 = Parrinello-Rahman        ; replaced
>>> 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
>>>
>>> I think this is the correct way to treat this type of system.
>>>
>>> Some might argue that a semi-isotropic p-coupling is the correct
>>> treatment for that. i.e.
>>>
>>> pcoupl                 = Parrinello-Rahman        ; replaced
>>> pcoupltype          = anisotropic
>>> tau_p                  = 5.0
>>> compressibility   = 4.5e-5  4.5e-5
>>> ref_p                   = 1.0     1.0
>>>
>>> where the first is for Z (the cylindrical axis of HII phase) and the
>>> second parameters control and scale the box size in both X and Y
>>> directions
>>> equally.
>>>
>>> I just like to know your opinions on this. Which one do you think is the
>>> better way to treat such systems?
>>>
>>> Thanks in advance for your comments.
>>> Mohsen
>>>
>>>
>>>
>>> --
>>> *Rewards work better than punishment ...*
>>>
>>>
>>
>>
>>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
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>
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-- 
*Rewards work better than punishment ...*