[gmx-users] Quick question about pressure coupling

[Justin Lemkul]

On 9/11/13 9:20 AM, HANNIBAL LECTER wrote:
> Yes
>

Then I would call your outcome an artifact of a physically unreasonable setup.

-Justin

>
> On Wed, Sep 11, 2013 at 9:18 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 9/11/13 9:09 AM, HANNIBAL LECTER wrote:
>>
>>> 500ps simulations. Yes everything is immersed in a bath of water. Can you
>>> please elaborate a little more as to why do you doubt semiisotropic
>>> coupling may not be necessary?
>>>
>>>
>> Water should compress isotropically.  I understand where you're coming
>> from, given that you have observed a seemingly semiisotropic compression of
>> the system, but physically that is not right.  Something like a membrane,
>> that has properties that make it sensible to couple x-y and z compression
>> separately, would use semiisotropic coupling.
>>
>> Is this a system in which you're using freezegrps?
>>
>> -Justin
>>
>>
>>> On Wed, Sep 11, 2013 at 9:05 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>>
>>>
>>>>
>>>> On 9/11/13 9:01 AM, HANNIBAL LECTER wrote:
>>>>
>>>>   I am trying to simulate a peptide inside a nanotube and using isotropic
>>>>> pressure coupling for the system. The nanotube is immersed in a cuboidal
>>>>> box of water and aligned along the z direction of the box.
>>>>>
>>>>> The XX, YY components of the stress tensor are about ~570 bars and the
>>>>> ZZ
>>>>> component is about -1179 yielding a total pressure of about 2 bars
>>>>> whereas
>>>>> my set pressure is ~1.01325 bars. Is this okay or should I be using
>>>>> semiisotropic coupling?
>>>>>
>>>>>
>>>>>   Over how long a time period are these values?  If everything is
>>>> immersed
>>>> in a bath of water, I doubt semiisotropic coupling is necessary.
>>>>
>>>> -Justin
>>>>
>>>> --
>>>> ==============================****====================
>>>>
>>>>
>>>> Justin A. Lemkul, Ph.D.
>>>> Postdoctoral Fellow
>>>>
>>>> Department of Pharmaceutical Sciences
>>>> School of Pharmacy
>>>> Health Sciences Facility II, Room 601
>>>> University of Maryland, Baltimore
>>>> 20 Penn St.
>>>> Baltimore, MD 21201
>>>>
>>>> jalemkul at outerbanks.umaryland.****edu <jalemkul at outerbanks.**
>>>> umaryland.edu <jalemkul at outerbanks.umaryland.edu>> | (410)
>>>> 706-7441
>>>>
>>>> ==============================****====================
>>>>
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>> --
>> ==============================**====================
>>
>> Justin A. Lemkul, Ph.D.
>> Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 601
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul at outerbanks.umaryland.**edu <jalemkul at outerbanks.umaryland.edu> | (410)
>> 706-7441
>>
>> ==============================**====================
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

==================================================