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
