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

[gromacs]

Yes. I should first run the 3x3x0.8 water to make the water

inequilibrium. 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.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20101217/fead9dea/attachment.html>