I had made a simulation box, and then after made two plates. During equilibration the atoms moves around the 'Z' axis of the simulation box.
As in zhi i had taken 10.
region allbox block -30 30 0 60 0 20
create_box 4 allbox
can anybody have any suggestion it will be very thankful to me.
Thanks in advance.
If you run MD at any finite temperature you would expect the atoms to move. Could you be clearer about what the problem is?
In case you want to restrict atoms to within a region, you can use some kind of a wall potential (e.g harmonic wall potential) to confine the atoms in a given axis. Just make sure you change the boundaries to be fixed in the direction of the wall.
It needs to be clarified from your query what you want.
From your query, what I understand:
If you want to fix your specific regional atom, you can use the below command:
group ### subtract g#### g1## g##2
group myall subtract all g1##
or,
fix ###l atom_type setforce 0.0 0.0 0.0
It is recommended to see the below article, where the authors have fixed one specific layer of their system. You can easily fix your atom using the above command for this type of case.
doi.org/10.1021/acsomega.0c03241
doi.org/10.1021/acs.langmuir.2c00734
If you express your problem clearly, I will try to help you from my sight as much as I know.
Thank You.
- Badges
- Science topic