[gmx-users] Quick question about pressure coupling

[HANNIBAL LECTER]

Would there be artifacts because of that?


On Wed, Sep 11, 2013 at 9:20 AM, HANNIBAL LECTER <hanniballecter13 at gmail.com
> wrote:

> Yes
>
>
> 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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