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 <vvcha...@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" <vvcha...@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 <ptf1...@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" <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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