Ok back to my first email. Can you brief for me the steps of setting Graphene oxide sheet on a simulation box with water. What i understood is to copy a script online and to put it on notepad then to copy the address and to run it through cmd. Please correct me if i am wrong
There's nothing brief about learning how to use LAMMPS, especially if
you are not familiar with using a unix/linux like operating system.
It could be tricky because you are trying to simulate a (relatively)
novel material which combines graphene with small organic molecules
and side-chains.
1) To run LAMMPS, you will need a command line terminal. LAMMPS is
not a graphical program. (Several graphical front ends have been
written for LAMMPS, but most of them are not free.)
https://lammps.sandia.gov/prepost.html
In addition, I recommend that if you are using windows, you should
install the BASH shell. I recommend installing virtualbox in windows
together with a debian-based linux distribution such as xubuntu. (The
following text was copied from another README file:) Alternatively,
if you are using Windows 10 or later, you can try installing the
"Windows Subsystem for Linux (WSL)", or "Hyper-V". Otherwise, if you
are using an older version of windows, try installing CYGWIN.
2) To use LAMMPS you will also need to install (and learn how to use)
a text editor. You need a text-editor to prepare the files that
LAMMPS will read. (Word, Wordpad, and Notepad will not work.)
Popular free text editors which you can safely install and run from
within the WSL terminal include: nano, ne, emacs, vim, and jove. If
you are not using WSL, you can also use a graphical text editor, such
as Atom, Sublime, Notepad++, VSCode,...
3) You will need to read papers that other people have written to find
out what is the best force-field for simulating Graphene oxide.
http://lmgtfy.com/?q=graphene+water+simulation
Here are several earlier discussions on the mailing list regarding this topic:
https://www.google.com/search?ei=SHJbXPzNDdHJ_wTClJ3ICQ&q=graphene+oxide+water+lammps&oq=graphene+oxide+water+lammps&gs_l=psy-ab.3...102873.233903..234399...0.0..0.82.871.12…0…1…gws-wiz…35i39j0i8i30j35i304i39j33i22i29i30j33i10.jo9i7Lzf4LM
https://lammps.sandia.gov/threads/msg32166.html
https://lammps.sandia.gov/threads/msg32418.html
https://lammps.sandia.gov/threads/msg80189.html
If you decide to use a force field intended for small organic
molecules (like OPLSAA or GAFF/GAFF2), then you will have to define at
least one new atom time to describe carbon in graphene. (I don't
think either OPLSAA or GAFF force field defines the properties of
graphene carbon.)
In addition, there are many popular water models you can choose from,
including SPCE, TIP3P, TIP4P, TIP5P, AMOEBA… You should choose the
one which is compatible with your model for graphene.
4) You will need to create a DATA file which describes the geometry
and bond connectivity (and angle topology, etc...) of the
graphene-oxide, as well as the water.
a) You can create your own DATA file manually. The file format of a
DATA file is explained here:
https://lammps.sandia.gov/doc/2001/data_format.html
b) You can use somebody else's software to build the DATA file. There
is a list of molecule builder programs. Here is that link again:
https://lammps.sandia.gov/prepost.html
c) I'm not sure this is helpful, but there is an example how to build
a simple graphene-water mixture located here:
http://moltemplate.org/visual_examples.html#nanotube+water
... However this example is not helpful because: i) there are no bonds
between the carbon atoms, ii) the carbon atoms are not allowed to
move, iii) this is graphene, not graphene-oxide. (Disclaimer: I wrote
moltemplate, but I'm not sure it is a good fit for what you are trying
to do.)
If you actually decide to use this example, you will have to modify it heavily.
To create graphene-oxide, it is possible to choose randomly from
different unit cells, each containing different side-groups (eg OH),
using the "new random" command in moltemplate (see chapter 7.8 of the
moltemplate manual for details.) However you will have to define
those side-groups yourself manually. (Only once, for each type of
side-group.)
Bonds between graphene carbon atoms?
Regardless of which molecule-builder tool you decide to use, I
suspect you might need to add explicit bonds between carbon atoms in
the graphene. If you allow the carbon atoms to move, then these bonds
will prevent the carbon atoms from drifting away during the
simulation. (Perhaps you don't need to allow these atoms to move?)
In addition, if you are using a user-customized version of a
force-field like OPLSAA to lookup angle, dihedral, and improper
parameters for the side-groups in graphene-oxide, then it might be
necessary to define bonds between these graphene-carbon atoms after
all. This is because the angles, dihedrals, and impropers for the
side-chain atoms generated by the force-field rules depend on how all
these carbons are bonded together. (This assumes you have modified
the file containing the force-field information include definitions of
the graphene carbons. If you decide to attempt this for OPLSAA, then
please email me to let me know how you did it. I'd be curious.)
Note: As far as I know, neither topotools, nor moltemplate knows
how to build a periodic crystalline material (like graphene or
graphene oxide) in either 2D or 3D if it containing bonds which cross
the periodic boundary conditions. If you need bonds between the
graphene carbon atoms, then you will have to add those bonds manually
at the periodic boundaries.
I hope this gives you a better idea what lies ahead.
Good luck.
Andrew