On 12/17/10, Mark Abraham <[email protected]> wrote: > > > On 12/17/10, gromacs <[email protected]> wrote: > > Yes. I should first run the 3x3x0.8 water to make the water > > > > > > in equilibrium. > > > > > > No. Any box dimension below about 2nm is nonsense with a normal force field. > > You want a film in vacuum, so use a box that is large enough to contain both > the film and enough vacuum that the films cannot feel each other. So your box > dimension in the direction normal to the film must be at least the thickness > of the film plus twice rcoulomb. >
Or, use pbc=xy. See manual 7.3.9 Mark > > > NVT will also be important for equilibration, per Vitaly's comments. > > You may also need to use a very short MD timestep - films are intrinsically > less stable than bulk solvent, and the "normal" values are all for bulk, > condensed media. > > Mark > > > > > > 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" <[email protected]> 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 <[email protected]> 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" <[email protected]> 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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