[gmx-users] water genbox 3x3x0.8 EM not successful T not high

[gromacs]

-------- Forwarding messages -------- From: gromacs <ptf1242 at 163.com> Date: 2010-12-17 12:48:55To:  vvchaban at gmail.com Cc:  gmx-users at gromacs.org Subject: Re:Re: water genbox 3x3x0.8 EM not successful T not high 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.

One problem is that how can i make the Energy Minimising successful?

There are some water molecules not in suitable position. 

If i have problem or success, i will give an answer to all. At 2010-12-17 09:51:57，"Vitaly Chaban" <vvchaban at 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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