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. > > >
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists