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

[Vitaly Chaban]

Another issue that you will get in future. With such a system you
should use NVT ensemble to maintain liquid-vapor interface in your
system. Generally, NPT also can be used, but before you need run NVT
anyway in order to create this liquid-vapor interface. Otherwise, the
system will collapse at the first steps.

Good luck.

Dr. Vitaly V. Chaban





On Fri, Dec 17, 2010 at 12:46 AM, Vitaly Chaban <vvchaban at gmail.com> wrote:
> 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.
>>
>>
>>
>> If i directly put the  3x3x0.8 water in the 3x3x9 box, i will try to see the
>> result.
>>
>>
>>
>> I
>>
>>
>>
>> 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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