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

[Mohsen Ramezanpour]

I did this test already, actually. The main problem I am facing right now
is that the semi-isotropic test systems get equilibrated (judging on box
size for now) after ca. 50 ns or less.
BUT for the anisotropic coupling, the box sizes 1) fluctuate a lot and 2)
does not seem to be equilibrated even after 300 ns. This makes me less
confident on the results, especially with the point you mentioned on
the effect of anisotropic after a long simulation time.


Cheers,
Mohsen

On Thu, Sep 28, 2017 at 5:51 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 9/28/17 12:31 AM, Mohsen Ramezanpour wrote:
>
>> 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.
>>
>
> It seems like you already have a rationale for what to do. In the absence
> of literature precedent, you should probably test both to confirm your
> suspicions and validate your approach. Just be aware of potential artifacts
> due to anisotropic pressure coupling. They can be quite extreme over the
> course of a long simulation.
>
> -Justin
>
>
> 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
>>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>>>
>>> ==================================================
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at http://www.gromacs.org/Support
>>> /Mailing_Lists/GMX-Users_List before posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-request at gromacs.org.
>>>
>>>
>>
>>
> --
> ==================================================
>
> 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
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==================================================
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>



-- 
*Rewards work better than punishment ...*