Respected Sir,
I want to make a data file for silver atoms.So,can you please guide me how to make a data file & what extension is used for the “data file”.How to feed all parameters in that file?
Regards,
Ritesh Satwani
Hi .
I think you can find what you need at these two link s :
1- http://lammps.sandia.gov/doc/2001/data_format.html
2-http://lammps.sandia.gov/doc/Section_tools.html
regards,
saeed.
The second link is useful if you are already familiar with CHARMM,
or AMBER, or Materials Studio. In that case, you can use the molecule
builders which come with those programs, and later can convert the
files generated by them into LAMMPS format.
However some of the programs (eg amber2lmp) are old, have bugs, and
are not maintained.
Otherwise, look here:
http://lammps.sandia.gov/prepost.html#builders
This link list includes some important programs (topotools, emc,
avogadro, ateph...)
As for the force-field parameters, if you want to have the maximum
amount of flexibility, I recommend putting the force-field parameters
in your LAMMPS input script file(s), instead of the data file. (This
is especially true if you want to use unusual force-field styles such
as pair_style tersoff, sw, table, ...) If you reload the input script
with these commands after restarting your simulation, this will insure
that the force-fields will remain consistent. (In my experience, the
files created by write_data and write_restart commands sometimes have
corrupted force-field information.)
(advertisement:) Some molecule builders don't help you choose
force-field parameters for your simulation. If you are simulating
organic molecules, then "moltemplate" has some tools to help generate
OPLSAA force-field parameters. (disclaimer: I wrote moltemplate.)
Finally, if you are simply simulating crystalline silver, (instead
of molecules with explicit bonds), then you might not need to use a
data file. You can build period crystalline systems using the
"create_atoms" command, and the "lattice" and "region" commands:
http://lammps.sandia.gov/doc/create_atoms.html
http://lammps.sandia.gov/doc/lattice.html
http://lammps.sandia.gov/doc/region.html
http://lammps.sandia.gov/doc/group.html
http://lammps.sandia.gov/doc/create_box.html
Hope this helps
Andrew
Here are two other programs which you should also take a look at:
http://projectaten.org/index.php?project=Aten
http://sourceforge.net/projects/moleculardynami/
(advertisement:) Some molecule builders don't help you choose
force-field parameters for your simulation. If you are simulating
organic molecules, then "moltemplate" has some tools to help generate
OPLSAA force-field parameters. (disclaimer: I wrote moltemplate.)
In addition to moltemplate.org, the new version of topotools might be
able to supply force-field information as well (using the CHARMM
force-field).
http://sites.google.com/site/akohlmey/software/topotools#TOC-Version-1.5
Cheers
Andrew