Good morning Lammps developers and list members:
I’m working for a program about doing biosorption simulation. It’s about simulating the process of the reaction between a protein(metallothionein) to seize a heavy metal ion like Cu2+ or Pb2+. I hope I can show my client a short video or some pictures from this process. I wonder if Lammps can help me with this.
What’s more, if Lammps can help me with this. What kind of input do I need to prepare? Like the structure of protein? Do I have to know the exact mechanism of the reaction?
Sincerely
Thanks!
Good morning Lammps developers and list members:
I'm working for a program about doing biosorption simulation. It's
about simulating the process of the reaction between a protein(metallothionein)
to seize a heavy metal ion like Cu2+ or Pb2+. I hope I can show my client a
short video or some pictures from this process. I wonder if Lammps can help
me with this.
What's more, if Lammps can help me with this. What kind of input do
I need to prepare? Like the structure of protein? Do I have to know the
exact mechanism of the reaction?
that depends on whether you want to simulate the exact science or just an
animation displaying the principle model.
in the first case, the answer is "probably yes", however, it is less a
question of whether LAMMPS is capable of this, but rather which kind of
force field is a suitable choice for your needs. this can best be found out
from studying the published literature. LAMMPS can provide a simulation
engine for many models, but it doesn't "know" which is the right model.
if you are just after a nifty animation, the answer would be that probably
a more animation oriented tool (Blender?) might be more suitable. in case
you want to use LAMMPS, you would still have to find a physical model that
is capable of representing the behavior of what you are looking for. you
would probably need some sort of biasing feature (e.g. via the colvars
module) to drive your system along the desired path. again, the majority of
the information you would need, can be obtained from the published
literature and the question then becomes: has LAMMPS the necessary
features, which you can find out from comparing what the model of choice
needs with what LAMMPS has available as described in the documentation.
axel.