Hi, all.
I am trying to simulate my system using coarse-grained MD in LAMMPS, and I have a very beginner’s question:
I know that I first need data file including coordination of all atom in the system.
but in coarse-grained MD, I will need coordinations of beads, right??
To create the coordination file (i.e., LAMMPS data file), would you please let me know what I can do ?
Can I just make it as xyz coordination file without appointing atom type?
Thanks.
dear anonymous (....),
Hi, all.
I am trying to simulate my system using coarse-grained MD in LAMMPS, and I
have a very beginner's question:
I know that I first need data file including coordination of all atom in the
system.
but in coarse-grained MD, I will need coordinations of beads, right??
To create the coordination file (i.e., LAMMPS data file), would you please
let me know what I can do ?
from the perspective of an MD program, there is no difference between
atoms and coarse grain beads. all it sees are positions with masses
and potentials.
Can I just make it as xyz coordination file without appointing atom type?
...and how should the MD code find out what to compute?
read your mind??
software has no imagination at all. it only does what you
tell it to do. if you feed it insufficient information, it will
complain or crash. if you feed it incorrect information it
will generate incorrect results or crash. if you run it wrong
it will waste your time or it will crash.
in short, it is your responsibility to be smarter than the
software that you are using and make sure your feed it
all it needs to produce correct results. just throwing some
data at it and hoping for the best won't work.
cheers,
axel.
Yes, you need input data file which is not xyz file. The data file format is well documented in read_data documentation section. There’re some sample programs in examples directory which can be used to create input data file.
You haven’t described clearly what kind of system you are interested in. That will be helpful to understand what level of coarse graining you are looking for. It’s highly advisable to go through some literature before starting simulation!