[gmx-users] Re: Re: Re: water genbox 3x3x0.8 EM not successful T not high

[Vitaly Chaban]

You SHOULD bring water to EQUILIBRIUM starting from 3x3x9 box with
water at the center of this box. You will NEVER get EQUILIBRIUM water
film using 3x3x0.8.




> Yes. I should first run the 3x3x0.8 water to make the water
>
> in equilibrium. And then i use editconf to put the water at the centre of
>
> 3x3x9 box, so the film was 0.8 nm, the Z dimension is 9 nm, so there will be
> film.
>
> I want to simulate the rupture of the thickness of water film.
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> If i directly put the  3x3x0.8 water in the 3x3x9 box, i will try to see the
> result.
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>
>
> I
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> At 2010-12-17 13:12:43，"Vitaly Chaban" <vvchaban at gmail.com> wrote:
>
>>I still do not understand what physical system you want to create in
>>the MD system or what phenomenon you want to reproduce.
>>
>>If you need a water film, then the only solution is to follow my
>>former suggestion.
>>
>>In no case should you use "3x3x0.8 NPT" MD box! If somebody suggested
>>you to do such thing, then this person simply does not understand
>>classical MD simulations.
>>
>>--
>>Dr.Vitaly V. Chaban
>>
>>
>>
>>
>>
>>
>>On Thu, Dec 16, 2010 at 11:48 PM, gromacs <ptf1242 at 163.com> wrote:
>>> OK. I will use your method. But i am afraid there will be something wrong. Because generally, i should run the 3x3x0.8 NPT water, and then i use editconf to add the water to 3x3x3. If i donot run 3x3x0.8, i may not be able to run the final interface box. Because the water in the box is not at proper situation or position. Anyway, i will have a try first.
>>>
>>> If i have problem or success, i will give an answer to all.
>>> At 2010-12-17 09:51:57，"Vitaly Chaban" <vvchaban at gmail.com> wrote:
>>>>>>Hey, gromacs -
>>>>>>
>>>>>>Nice to hear from you here... It is a bad idea to simulate something
>>>>>>with any cartesian dimension lower than a couple of nanometers using
>>>>>>classical FFs.  All your problems are generated by 0.8 nm of the
>>>>>>z-side.
>>>>>>
>>>>>>--
>>>>>>Dr. Vitaly V. Chaban
>>>>>>Rochester, U.S.A.
>>>>>>
>>>>>
>>>>> Thanks very much. I use the cutoff=0.38, because the cutoff should be smaller than the half box size. I guess it may be the Z dimension is too small, Plus the PBC. But when i use 1.8x1.8x1.8nm bulk water, all results are OK.
>>>>>
>>>>> My teacher wants me to simulate 3x3x0.8, 3x3x0.9 nm water film's rupture. So i have to run bulk >3x3x0.8 water and then add box to 3x3x9 to form interface.
>>>>>
>>>>> So if i want to run run bulk 3x3x0.8 water, how could i do? which FF should i use? the high T may be >due to EM not success??
>>>>
>>>>
>>>>I believe you use the term "bulk water" in another sense as compared
>>>>to all other guys here. When people say "bulk liquid" they imply the
>>>>endless ocean of this liquid. It is not important what particular side
>>>>lengths you have, since due to PBC you get infinitively large system.
>>>>
>>>>I suspect your teacher wants you to obtain a film of water that would
>>>>be about 3 molecular layers wide. That's easy. Take your current box
>>>>of water and apply editconf -
>>>>
>>>>editconf -f <current_conf> -o <water_film_conf> -box 3 3 3
>>>>
>>>>Finally, just start MD run with a water_film_conf. You'll have the
>>>>same periodic box , but water molecules will be present only at its
>>>>center surrounded by vacuum in one (Z) direction.
>>>>
>>>>Happy GROMACSing,
>>>>
>>>>Dr. Vitaly V. Chaban
>>>>Rochester, U.S.A.
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