Dear LAMMPS users,
I’m going to build a simulation of water behavior with a Graphene oxide-Zif8 composite. The problem is the domain of the system is too large (20x20x15 nm3) and thus I’m thinking about doing coarse-graining of water molecules. However, I want to maintain the atom structure of the GO/MOF composite.
I would like to ask whether it is possible to have coarse-grained atom and full-atom in a LAMMPS simulations? Have anyone done that before in the literature?
Thanks a lot.
Hieu
Dear LAMMPS users,
I'm going to build a simulation of water behavior with a Graphene
oxide-Zif8 composite. The problem is the domain of the system is too large
(20x20x15 nm3) and thus I'm thinking about doing coarse-graining of water
molecules. However, I want to maintain the atom structure of the GO/MOF
composite.
200x200x150 A^3 isn't really that large for a code like LAMMPS. a quick
back of the envelope guesstimate would make this a system with less than 1
million atoms. LAMMPS is capable of running simulations with *billions* of
atoms (and people have done it). you simply may have to look for a larger
parallel machine to run your simulation.
I would like to ask whether it is possible to have coarse-grained atom and
full-atom in a LAMMPS simulations?
yes, technically it is possible. LAMMPS doesn't care whether the simulated
(point) particles represent a single or multiple atoms. it just applies to
model you provide, computes the forces and moves the particles.
the tricky thing is to determine a suitable parameterization and figure out
whether this is representing what you want to model well enough.
specifically water is a tricky issue. in many cases, the interactions of
individual water molecules with your substrate are crucial to be
represented explicitly, e.g. to be able to have hydrogen bonds, and thus a
coarse grain water representation (as good as it may be to represent bulk
water), may not be suitable for your setup.
Have anyone done that before in the literature?
IIRC, people in the group of mario orsi have done mixed coarse-grain /
all atom simulations as i recall integrating some code into the r-RESPA
integrator in LAMMPS to make it more efficient.
nobody here is going to do a literature search for you, so you have to get
your hands dirty and search for it yourself.
axel.