Is anybody made water molecule through lammps lattice command. what is the way to create water molecules? how to simulate interaction between water and a metal wall? please give any idea to do this simulation.
Thanks and regards
Karthik V
Karthik,
As far as I know, the lattice command can’t be used to build a water crystal as you suggest. The replicate command is better suited for the task you have in mind. Even so, you’ll need to build the first water molecule yourself, or get it from somewhere. Take a look at the discussion in the manual on building water:
http://lammps.sandia.gov/doc/Section_howto.html#4_7
As far as the water-metal interaction, you’ll have to start by finding an appropriate force field from the literature that does a reasonable job modeling the specific interaction you want.
Paul
Is anybody made water molecule through lammps lattice command. what is the
the easiest way to create a bulk molecular system is to start from
a small data file input (generated manually or with a small program
or script) and then replicate it to the desired size. if you start from
an unequilibrated configuration, you have to be careful to first break
symmetries (through heat) and then equilibrate, replicate, equilibrate,
replicate until you have what you need. equilibration with a small system
is _much_ faster and more efficient than with a large system.
way to create water molecules? how to simulate interaction between water and
a metal wall? please give any idea to do this simulation.
have you looked into the literature? there are a number of models
to represent metals and to represent the interaction between water
and metals. you should make a survey to find what is successful and
close to what you need. as always in simulations, there is no
one-size-fits-all solution.
cheers,
axel.
thank you for your replies Paul, Axel and Farrokh.
If i use the read_data command to read the data file, how can I create water droplet using region command without defining lattice?
Thanks and regards
Karthik V
thank you for your replies Paul, Axel and Farrokh.
If i use the read_data command to read the data file, how can I create water
droplet using region command without defining lattice?
once you have read in your data file, you have your system,
you cannot use it like a lattice. you can define regions in
box dimension coordinates as well, since the region selection
language is not flexible enough for this.
this is easiest (IMNSHO) done using VMD using its
embedded tcl script interpreter.
- load a large enough, pre-equilibrated (cubic?) water box
- translate it, so that the center of mass is at the origin
- create an atom selection that selects water molecules
with a given radius around the origin (the selection text would
look somewhat like this
: "same residue as ((name OH2) and (sqrt(x*x+y*y+z*z) < 10.0))"
- write the selection to some file and covert to a data file,
or create a data file from it directly using the topotools plugin.
cheers,
axel.
The region command does not require a lattice definition - see the
units box option. To input a set of water molecules into LAMMPS,
you will need to read them in from a data file - you can't create
them on the fly.
Steve