self assembly using LAMMPS

I am working on a project and I am trying to do it with LAMMPS. this is the first time I am using LAMMPS.

I am trying to simulate a self assembly procedure of two different type of nano particles, both in one simulation box. one of them is about 10nm and another one is 100nm. The challenging part is these two particles are coated with another material so they absorb each other and there is a force field between them due to this coating, these two particles are polarized in a magnetic field and we are going to do this self assembly in presente of a magnetic field, so another force field id added because of the polarization, and an external source of force is present because of the field. so all I am asking is can I simulate this phenomena in LAMMPS? do you have any suggestion for me?

I am working on a project and I am trying to do it with LAMMPS. this is the
first time I am using LAMMPS.

I am trying to simulate a self assembly procedure of two different type of
nano particles, both in one simulation box. one of them is about 10nm and
another one is 100nm. The challenging part is these two particles are coated
with another material so they absorb each other and there is a force field
between them due to this coating, these two particles are polarized in a
magnetic field and we are going to do this self assembly in presente of a
magnetic field, so another force field id added because of the polarization,
and an external source of force is present because of the field. so all I am
asking is can I simulate this phenomena in LAMMPS? do you have any
suggestion for me?

my suggestion:

step 0: apply for an extension to your deadline
step 1: learn how to do MD well for atoms and/or small molecules
step 2: learn some statistical mechanics and computing free energy and
using collective variable methods
step 3: learn how to do self-assembly with (polar) molecules
step 4: learn proper C++ programming
step 5: implement a fix into lammps that can apply a magnetic field
step 6: learn how to parameterize the missing force field parameters
step 7: run your self-assembly simulations in LAMMPS
step 8: celebrate

axel.

This is the main problem:

step 5: implement a fix into lammps that can apply a magnetic field

LAMMPS does not understand magnetic dipoles.
Take a look at this web page:
http://lammps.sandia.gov/doc/pair_dipole.html

You can run simulations in LAMMPS with dipole particles, but they are
electric, not magnetic. Although the force due to either type of
dipole has the same form, the dipoles implemented in LAMMPS will
change their orientation in response to a nearby charged atom. I
don't think there is a way to prevent that in LAMMPS without editing
the code (see below).

I am guessing that this is the main problem trying to simulate
magnetic materials in LAMMPS.

I could be completely wrong about this, so I hope someone will correct
me if I am. (Most LAMMPS users simulate particles at temperatures low
enough that they can ignore the magnetic field they generate. I am
also assuming that the force due to a static magnetic field on a
moving charged atom is negligible compared to the inter-atomic
pairwise forces. If not, then LAMMPS might not be the right program
to use. In that case, perhaps you should look at the software people
use to simulate plasmas.)

If I am correct, and if all of the particles in your simulation which
have magnetic moments also have zero charge, then I think it would be
sufficient to use "pair_style dipole/cut" and simply turn off the
dipole-charge ("Eqp") interactions between your dipoles and the
surrounding charges.

Alternately, if you want to write your own "pair_style
dipole/mag/cut", that would be nice too.

What code should you edit?
I cd to the "src" directory where LAMMPS is installed and type:
grep "dipole/cut" *.cpp */*.cpp
I get:
DIPOLE/pair_dipole_cut.cpp
GPU//pair_dipole_cut_gpu.cpp

So take a look at DIPOLE/pair_dipole_cut.cpp, and try to turn off the
dipole-monopole interactions.

If this is a bad idea, hopefully somebody will reply.
Cheers.

Andrew

I just remembered that ESPResSo (and ESPResSo++?) support magnetic dipoles:

http://espressomd.org/
http://www.ohloh.net/p/espressopp

Cheers
Andrew