[gmx-users] air-water-interface

[Nawel Mele]

Thanks a lot for your answer.
So by increasing the z coordinate after solvated the system we induce
creation of a empty space above the solvated box.
After minimisation a few water molecules move above its new empty space
because their link are not strong enough.


2013/5/13 Justin Lemkul <jalemkul at vt.edu>

>
>
> On 5/13/13 8:01 AM, Nawel Mele wrote:
>
>> So we just compute an interface vacuum-water like the picture in attach in
>> increase the coordinate value of the z-axis of the box?
>>
>
> The list does not accept attachments.  If you want to post an image or
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>
>
>  BUt I don't understand how just like that we creat an empty place and
>> water
>> move to this place??
>>
>>
> Seems like intuitive behavior to me.  Think about basic physics and
> thermodynamics.
>
> -Justin
>
>
>>
>> 2013/5/13 Justin Lemkul <jalemkul at vt.edu>
>>
>>
>>>
>>> On 5/13/13 6:10 AM, Nawel Mele wrote:
>>>
>>>  Hi all,
>>>>
>>>> I am performing a simulation of protein at air/water interface.
>>>>
>>>> For create an air-water interface I just expand the box in the z
>>>> direction.
>>>> So,aAfter minimization we can noticed that water molecules moved out of
>>>> bulk water in the z direction.
>>>>
>>>> Why you just need to expand the z-axis for obtain this interface?? I
>>>> don't
>>>> understand the mechanism.
>>>>
>>>>
>>>>  You're not creating an air-water interface by doing this, you're
>>> creating
>>> an vacuum-water interface and your water molecules are evaporating into
>>> the
>>> empty space.
>>>
>>> -Justin
>>>
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> --
> ==============================**==========
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
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-- 
*Mlle* Mele Nawel
Master 2 In Silico Drug Design
University of Paris Diderot/Strasbourg