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" <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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