Data file

Respected Sir
I want to know how to create supercell in different ratio. for example CL20/RDX 1:2,1:3,1:4…which software i want to choose. how to create supercell in different molecular ratio. I am using in lammps replicate option but molecule only doubled i cant able to create in different ratio.I hope you will do the needful.
Thanking you

Respected Sir
             I want to know how to create supercell in different ratio.
for example CL20/RDX 1:2,1:3,1:4.....which software i want to choose. how
to create supercell in different molecular ratio. I am using in lammps
replicate option but molecule only doubled i cant able to create in
different ratio.I hope you will do the needful.

​there is no general answer to this. it all depends on the details of the
structural arrangements, the kind of mixing, the size of the system, the
physical state (solid/liquid/gas)​, and the purpose you need the
equilibrated structure for. there are multiple ways to use LAMMPS to build
such structures, other cases are most easily done by writing custom scripts
or using tools like packmol, moltemplate, material studio, or handwritten
custom scripts.

axel.

Thanks. I don’t know if this helps, but check out the ethylene+benzene moltemplate example, currently located at:

https://github.com/jewettaij/moltemplate/tree/master/examples/all_atom/force_field_OPLSAA/ethylene%2Bbenzene_PACKMOL

(A version of this example may also be included in the “tools/moltemplate/examples” subdirectorywork included with lammps.)

You can control the simulation box size and number of molecules by editing the “mix_ethylene+benzene.inp” file (located in the “packmol_files” subdirectory I this example):
Here’s an excerpt:

structure ethylene.xyz


  number 1000 
  inside box 0. 0. 0. 80. 80. 80. 
end structure

structure [benzene.xyz](http://benzene.xyz)
  number 500
  inside box 0. 0. 0. 80. 80. 80. 
end structure

(As you can see, you must have PDB or XYZ files containing the geometry of each type of molecule.)

Packmol is only used to build the geometry. You must also share this information with the program you are using to build your LAMMPS data and input filea (which contain topology, charge, and force field information).

If you are using MOLTEMPLATE for this, then you would do this by editing “system.lt” file (located in the “momtemplate_files” subdirectory. Excerpt:


import "[ethylene.lt](http://ethylene.lt)"  # <- defines the "Ethylene" molecule type.
import "[benzene.lt](http://benzene.lt)"  # <- defines the "Benzene" molecule type.

Create 1000 ethylenes and 500 benzenes


# List them in the same order they appear in the PACKMOL .inp file(s).

ethylenes = new Ethylene[1000]
benzenes  = new Benzene[500]

# Periodic boundary conditions:

write_once("Data Boundary") {
   0.0  80.00  xlo xhi
   0.0  80.00  ylo yhi
   0.0  80.00  zlo zhi
}

This example uses the OPLSAA force field whose parameters have been converted into moltemplate format (and are stored in the “oplsaa.lt” file which is referenced in the “ethylene.lt” and “benzene.lt” files). You can also use COMPASS, and Amber(GAFF/GAFF2. (Although the publicly disclosed set of the COMPASS force field parameters and atom types is incomplete, and and you must manually assign partial charges to atoms if you use GAFF/GAFF2. As for COMPASS, we are hoping to release the full set of parameters soon.) You can also invent your own force field (by creating a new file similar to the the “oplsaa.lt” file) or hard-code your parameters I to your molecules directly.

Cheers

Andrew

P.S. You don’t have to use PACKMOL to create the geometry. You can specify molecule positions within moltemplate .lt files. There’s another version of this example using this approach which is located here:
https://github.com/jewettaij/moltemplate/tree/master/examples/all_atom/force_field_OPLSAA/ethylene%2Bbenzene

Another example:
http://www.moltemplate.org/visual_examples.html#nanotube+water