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Re: [lammps-users] fix NPT and fix move
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Re: [lammps-users] fix NPT and fix move

From: liyi bai <liyibai2011@...24...>
Date: Thu, 12 Apr 2018 11:49:17 +0900

Dear Axel,

Thank you very much for your suggestion and kindly remind.

I also tried to leave "fix move" away.But the plates will be change the position which I should avoid the situation .
Actually, I want to control the distance between two plates as a constant.So the position most not be moved.That's why I want to use fix move to fix the two plates.In detail,  lateral size of one larger plate as same as box size,other plate is much smaller  the boxsize.

I want to  keep the lateral size of  the box always as a constant I set up initially.For that, I adjust the system pbc only on Z direction during npt simulation by using below command line.However,the water will go through the plate and goes to other pbc box during NPT.Could you please point out some problems about the issue?

fix      7   water   npt temp $T $T 100.0 z 1.0 1.0 100.0  dilate all 

Thank you very much

best wishes


2018-04-11 22:43 GMT+09:00 Axel Kohlmeyer <akohlmey@...24...>:
On Wed, Apr 11, 2018 at 9:35 AM, liyi bai <liyibai2011@...29....> wrote:
> Dear all.
> I want to run MD simulation with NP(z)T ensemble for system of two plates
> immersed in water.
> I am wondering that the correct way combine fix npt  and fix move command.

there is no point in using fix move, when you don't move the atoms.
you can just leave those fixes away.

> I wrote input below,I am not sure if it is correct. Can any one give me some
> suggestion?

if you are not sure that something is working as expected, you should
construct test cases and monitor those carefully to see, if things
happen to your expectations. with carefully crafted tests, you can
check each feature you worry about individually.

asking the mailing list to help you with this is very risky. what if
the person responding makes a mistake? or overlooks something
important? or you are leaving out important information that would
have resulted in a different recommendations?
it is always your reputation and credibility that is on the line, if
you use your results in publications, so you need to verify for
yourself that you are simulating what you think and want to do.


> fix      6   water   shake 0.0001 20 0 b 1 a 1
> fix      7   water   npt temp $T $T 100.0 z 1.0 1.0 100.0  dilate all    #
> control system only on z direcation
> fix      8   plates1       move linear 0.0 0.0 0.0 units box   #fix plates 1
> fix      9   plates2       move linear 0.0 0.0 0.0 units box   #fix plates 2
> Thank you very much
> best wishes
>  liyi
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Dr. Axel Kohlmeyer  akohlmey@...43...4...
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.