-------- Forwarding messages -------- From: gromacs <ptf1...@163.com> Date:
2010-12-17 12:48:55To: vvcha...@gmail.com Cc: gmx-users@gromacs.org Subject:
Re:Re: water genbox 3x3x0.8 EM not successful T not high 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.
One problem is that how can i make the Energy Minimising successful?
There are some water molecules not in suitable position.
If i have problem or success, i will give an answer to all. At 2010-12-17
09:51:57，"Vitaly Chaban" <vvcha...@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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