I am new in LAMMPS as well as in MD simulation. However, I am trying to
start my simulation research with LAMMPS. I need very clear idea about some
besic steps of simulation by LAMMP.
1. I have setup LAMMPS by cygwin in my cpu and I did not make any
additional packages. So I just want confirm that whether the setup is OK or
it depends. from what you describe below, probably not. please study
2. I have build a model with graphene and CO2 for a simple simulation. But
I am confuse about running simulation. I think I need to obey some steps to
run a simulation. I just build the structures with Material studio. then
what will be my further steps to run a perfect simulation?
there is no such thing as a perfect simulation and what you describe as "a
simple simulation" is not that simple at all, but already quite complex
through requiring multiple atom types, an explicit bond topology and
long-range electrostatics. your best way to learn MD basics is to start
with atomic systems having only one type of atom. the classic system would
be liquid argon, then move on to small molecules, e.g. water, methane or
co2. methane may be particularly interesting, as it can be modeled as a
united atom model (i.e. with just one site like argon) and as an all atom
model and you can compare the results.
beyond that, you need to learn MD basics and thus what to do from a
combination of discussing with people experienced in MD, studying text
books on MD, reading the LAMMPS documentation, studying existing LAMMPS
tutorials and introductions, and reproducing published results. building
geometries is only the beginning. there are too many more individual steps
to list and describe/explain them all here. it won't hurt to take a class
in statistical mechanics, too.
3. I have found a data file is need to run a simulation in LAMMPS, how can
I build the data file of my model with GAFF force field.What is the step by
step procedure to do this.
please see my answer to point 3. also please keep in mind, that this is a
mailing list to support the LAMMPS software and not a classroom to learn
(basic) MD. similarly, the LAMMPS documentation describes how to use
LAMMPS, not how to do MD. it expects, that you have learned this *before*
starting with LAMMPS.