<html><head></head><body><div style="font-family: Verdana;font-size: 12.0px;"><div>I was under the impression a vacumn, or even gas/liquid interface becomes uniform molecule wise in such simulations due to scale. Thus, the applied pressure and other corrections necessary to set up the interface on a small scale, such as caclulated force at an imaginary interface for given gas/liquid systems? I wounder though, is it possible to give the pressure corrections a direction (a single wall instead of the entire unit cell)?
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<div style="margin:0 0 10px 0;"><b>Gesendet:</b> Montag, 13. Mai 2013 um 14:16 Uhr<br/>
<b>Von:</b> "Nawel Mele" <nawel.mele@gmail.com><br/>
<b>An:</b> "Discussion list for GROMACS users" <gmx-users@gromacs.org><br/>
<b>Betreff:</b> Re: [gmx-users] air-water-interface</div>
<div name="quoted-content">Thanks a lot for your answer.<br/>
So by increasing the z coordinate after solvated the system we induce<br/>
creation of a empty space above the solvated box.<br/>
After minimisation a few water molecules move above its new empty space<br/>
because their link are not strong enough.<br/>
<br/>
<br/>
2013/5/13 Justin Lemkul <jalemkul@vt.edu><br/>
<br/>
><br/>
><br/>
> On 5/13/13 8:01 AM, Nawel Mele wrote:<br/>
><br/>
>> So we just compute an interface vacuum-water like the picture in attach in<br/>
>> increase the coordinate value of the z-axis of the box?<br/>
>><br/>
><br/>
> The list does not accept attachments. If you want to post an image or<br/>
> file, provide a public link to access it.<br/>
><br/>
><br/>
> BUt I don't understand how just like that we creat an empty place and<br/>
>> water<br/>
>> move to this place??<br/>
>><br/>
>><br/>
> Seems like intuitive behavior to me. Think about basic physics and<br/>
> thermodynamics.<br/>
><br/>
> -Justin<br/>
><br/>
><br/>
>><br/>
>> 2013/5/13 Justin Lemkul <jalemkul@vt.edu><br/>
>><br/>
>><br/>
>>><br/>
>>> On 5/13/13 6:10 AM, Nawel Mele wrote:<br/>
>>><br/>
>>> Hi all,<br/>
>>>><br/>
>>>> I am performing a simulation of protein at air/water interface.<br/>
>>>><br/>
>>>> For create an air-water interface I just expand the box in the z<br/>
>>>> direction.<br/>
>>>> So,aAfter minimization we can noticed that water molecules moved out of<br/>
>>>> bulk water in the z direction.<br/>
>>>><br/>
>>>> Why you just need to expand the z-axis for obtain this interface?? I<br/>
>>>> don't<br/>
>>>> understand the mechanism.<br/>
>>>><br/>
>>>><br/>
>>>> You're not creating an air-water interface by doing this, you're<br/>
>>> creating<br/>
>>> an vacuum-water interface and your water molecules are evaporating into<br/>
>>> the<br/>
>>> empty space.<br/>
>>><br/>
>>> -Justin<br/>
>>><br/>
>>> --<br/>
>>> ==============================****==========<br/>
>>><br/>
>>><br/>
>>> Justin A. Lemkul, Ph.D.<br/>
>>> Research Scientist<br/>
>>> Department of Biochemistry<br/>
>>> Virginia Tech<br/>
>>> Blacksburg, VA<br/>
>>> jalemkul[at]vt.edu | (540) 231-9080<br/>
>>> <a href="http://www.bevanlab.bioche" target="_blank">http://www.bevanlab.bioche</a>m.****vt.edu/Pages/Personal/justin<<a href="http://vt.edu/Pages/Personal/justin" target="_blank">http://vt.edu/Pages/Personal/justin</a>><br/>
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>>><br/>
>>><br/>
>><br/>
>><br/>
>><br/>
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>><br/>
> --<br/>
> ==============================**==========<br/>
><br/>
> Justin A. Lemkul, Ph.D.<br/>
> Research Scientist<br/>
> Department of Biochemistry<br/>
> Virginia Tech<br/>
> Blacksburg, VA<br/>
> jalemkul[at]vt.edu | (540) 231-9080<br/>
> <a href="http://www.bevanlab.bioche" target="_blank">http://www.bevanlab.bioche</a>m.**vt.edu/Pages/Personal/justin<<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a>><br/>
><br/>
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<br/>
<br/>
<br/>
--<br/>
*Mlle* Mele Nawel<br/>
Master 2 In Silico Drug Design<br/>
University of Paris Diderot/Strasbourg<br/>
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