Hi, everyone.
It looks like coarse grained molecular dynamics can be done with LAMMPS.
yes. typical coarse grain molecular dynamics is effectively the same
as all-atom MD, the only difference is that one particle (or bead) represents
multiple atoms. there are several coarse grain models in the published
literature with different parametrizations and functional forms. many use
conventional 12-6 lennard-jones potentials, some lj with other exponents,
some use many-body terms, some simple harmonic potential networks.
But I hardly find an example including input script, data file, and etc for
CGMD with LAMMPS.
there is an example for the coarse grain model that our
group is working on. check out.
http://www.temple.edu/cst/icms/surfactants.html#cgmodel
So, I was wondering if anybody could provide me sample input script, data
file, and etc for CGMD?
before looking at inputs, i strongly suggest to have a closer look
at the literature and applications of coarse-grain models, as well
as checking out its benefits and shortcomings. you cannot learn
that from some inputs and yet you need to understand this well
before starting any real simulations, or else you will be wasting
your time.
by the way,
1.
for CGMD, what the atom-style should be ?
depends.
since a system of my interest includes two different molecules, can I use
two types like typing both:
atom_style angle
atom_style atomic
no. just use angle. that includes atomic.
2.
Can I assign charge onto a coarse-grained bead?
yes.
If so, could anyone let me know how to?
through the normal ways as it is done in lammps,
either a data file or through set commands in the
input script. you only have to make sure that your
atom style is able to store charge information, i.e.
most likely you'll need to use atom_style full.
BTW: none of this is in any way specific to coarse
grain MD. to learn how to deal with this many of
the existing inputs in the example folder are just
as relevant, regardless of whether they represent
a coarse grain system.
cheers,
axel.