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)?
Gesendet: Montag, 13. Mai 2013 um 14:16 Uhr
Von: "Nawel Mele" <nawel.m...@gmail.com>
An: "Discussion list for GROMACS users" <gmx-users@gromacs.org>
Betreff: Re: [gmx-users] air-water-interface
Von: "Nawel Mele" <nawel.m...@gmail.com>
An: "Discussion list for GROMACS users" <gmx-users@gromacs.org>
Betreff: Re: [gmx-users] air-water-interface
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 <jalem...@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
> file, provide a public link to access it.
>
>
> 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 <jalem...@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
>>>
>>> --
>>> ==============================****==========
>>>
>>>
>>> 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://vt.edu/Pages/Personal/justin>
>>> <h**ttp://www.bevanlab.biochem.vt.**edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>> >
>>>
>>> ==============================****==========
>>>
>>> --
>>> gmx-users mailing list gmx-users@gromacs.org
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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>
>
> ==============================**==========
> --
> gmx-users mailing list gmx-users@gromacs.org
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--
*Mlle* Mele Nawel
Master 2 In Silico Drug Design
University of Paris Diderot/Strasbourg
--
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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 <jalem...@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
> file, provide a public link to access it.
>
>
> 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 <jalem...@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
>>>
>>> --
>>> ==============================****==========
>>>
>>>
>>> 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://vt.edu/Pages/Personal/justin>
>>> <h**ttp://www.bevanlab.biochem.vt.**edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>> >
>>>
>>> ==============================****==========
>>>
>>> --
>>> gmx-users mailing list gmx-users@gromacs.org
>>> http://lists.gromacs.org/****mailman/listinfo/gmx-users<http://lists.gromacs.org/**mailman/listinfo/gmx-users>
>>> <htt**p://lists.gromacs.org/mailman/**listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
>>> >
>>> * Please search the archive at http://www.gromacs.org/**
>>> Support/Mailing_Lists/Search<h**ttp://www.gromacs.org/Support/**
>>> Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>>before
>>> posting!
>>>
>>> * Please don't post (un)subscribe requests to the list. Use the www
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>>> * Can't post? Read http://www.gromacs.org/****Support/Mailing_Lists<http://www.gromacs.org/**Support/Mailing_Lists>
>>> <http://**www.gromacs.org/Support/**Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>>> >
>>>
>>>
>>
>>
>>
>>
>>
> --
> ==============================**==========
>
> 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>
>
> ==============================**==========
> --
> gmx-users mailing list gmx-users@gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
> * Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
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> * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>
--
*Mlle* Mele Nawel
Master 2 In Silico Drug Design
University of Paris Diderot/Strasbourg
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
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