how to built a system of two phase

Hi all
I want to build a system of two phase, one is a periodic mineral layer, the other is a liquid phase which is in contact with the mineral layer, to simulate the adsorption of ions in the solution to mineral surface. I have the XYZ coordinates of the mineral, for the solution, should I build a box filled with water and ions? How can I make the two phases in contact? Is there any other details should I pay attention to in the simulation?

Thank you!

Jingjing

LAMMPS doesn't have commands to build molecular
systems. You need to use some other builder program
that will create molecular topolgies (e.g for the water)
and output a file that can be converted to LAMMPS
input, e.g. a data file. There are tools in the
tools dir that will do format conversions, e.g. ch2lmp
will convert PDB files into LAMMPS data files.

Steve

Hi all
I want to build a system of two phase, one is a periodic mineral layer, the
other is a liquid phase which is in contact with the mineral layer, to
simulate the adsorption of ions in the solution to mineral surface. I have
the XYZ coordinates of the mineral, for the solution, should I build a box
filled with water and ions? How can I make the two phases in contact? Is
there any other details should I pay attention to in the simulation?

first you should set up each part separately, e.g. by building
a system with the final dimensions, but placing a LJ wall where
the other phase would be. that will allow you to test and debug
the settings for each part separately.

when merging the two subsystems, check this out for an example:
http://sites.google.com/site/akohlmey/software/topotools/topotools-tutorial---various-tips-tricks#TOC-Combine-multiple-data-files-with-ov

you have to pay special attention to the interface layer,
since the merge will be a huge disruption of the atoms
near the interface. one way to deal with it is to first run
a minimization and then use e.g. fix spring/self on the
atoms near the interface and then gradually reduce the
spring constant to the let the system relax smoothly
without generating huge shockwaves that would travel
through your system indefinitely due to periodicity.

cheers,
     axel.