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

[Vitaly Chaban]

>>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.