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

[gromacs]

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.