Intial geometry of simulation using LAMMPS

Dear Users,

I have a very basic question regarding the geometry of simulation cell.
Please give me some idea about how to generate the geometry in which crystalline cuboid of oxide material has to kept in the center of simulation box while the rest of the space filled with water molecules? or i have to use pizza.py tool. Please guide me.

Thank you.

Regards

Gaganpreet
Panjab University,

Chandigarh

If you have a well-defined structure that you can define, programs such as Packmol combined with VMD can generate the LAMMPS data file. You’ll need to specify the force field parameters on your own, however.

—ÅEI

Dear Users,

I have a very basic question regarding the geometry of simulation cell.
Please give me some idea about how to generate the geometry in which
crystalline cuboid of oxide material has to kept in the center of simulation
box while the rest of the space filled with water molecules? or i have to
use pizza.py tool. Please guide me.

you need to do some scripting/programming for that.
usually for systems like yours, you'd generate two
separate initial systems, one for each component.
check out the model/force field for it and equilibrate
and then combine the two geometries. one possible
route is shown here.

https://sites.google.com/site/akohlmey/software/topotools/topotools-tutorial---various-tips-tricks#TOC-Combine-multiple-data-files-with-ov

mind you, this is not something that is newbie-proof.
you have to be careful and know what your are doing
and monitor carefully what is happening. merging two
different systems requires to extra effort where you
cut out a piece and replace it with something else.
you have to avoid overlaps and "heal" the interface
region, before you can do a regular MD. if you are
not careful, you can produce complete nonsense
and your results may be tainted, e.g. by travelling
shockwaves (which don't die down easily due to
periodic boundary conditions).

cheers,
    axel.

This is another alternative.

  1. Start with water box (with known number of atoms that you want) and equilibrate it., Then use fix intend command with sphere or cylindrical setting and create an empty space within water box. Save the restart file and convert it to data format
  2. Write out the lammps file for the oxide you have separately with oxide parameters.
  3. Merge them ( I think Axel mentioned it in last email).
  4. Re-equilibrate your system with Oxide fixed and water (NPT). Water will start interacting with the oxide
  5. Remove the constraint from the oxide and equilibrate further to track if all the thermodymic quantities make sense.