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

Justin Lemkul jalemkul at vt.edu
Thu Sep 28 02:26:22 CEST 2017



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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