Hello All,
I am trying to prepare input files for ReaxFF forcefield simulations. I have an simbox.xyz file generated using packmol. It seems ReaxFF does not need bonds and angles in the data file. I want to generate a data files with just coordinates, please let me know how we can do this. Also can we use ReaxFF force fields with Quartz surfaces.
Thank you very much for the help.
Best,
Hari Katepalli PhD
Post-Doctoral Associate
Hatton & Blankschtein Groups
Department of Chemical Engineering
Massachusetts Institute of Technology
Cambridge, MA 02139
USA
If you have a LAMMPS data file with bonds/angles/etc,
then just open it in an editor and remove those
portions. If you want to automate that, then if
you are using PackMol to create the LAMMPS data
file, that’s a PackMol question.
You can use ReaxFF with any material it has
been parameterized for. The pair reax doc page
explains where to look for ReaxFF parameter files
if they are not included with LAMMPS.
Steve
Hello All,
I am trying to prepare input files for ReaxFF forcefield simulations. I
have an simbox.xyz file generated using packmol. It seems ReaxFF does not
need bonds and angles in the data file. I want to generate a data files
with just coordinates, please let me know how we can do this. Also can we
use ReaxFF force fields with Quartz surfaces.
the format of the LAMMPS data file is fairly simple and described in
detail in the documentation for the read_data command.
depending on the required level of sophistication, you may be able to
generate a suitable data file with a little bit of script programming
(shell script, awk, perl, tcl, python, matlab etc.).
if you are familiar with using VMD and its script interface, you might
consider using the topotools plugin. topotools simplifies topology
generation and manipulation, but can also be used to remove topology
information. it also is able to read and write most flavors of LAMMPS data
files.
axel.
Hello All,
I am trying to prepare input files for ReaxFF forcefield simulations. I have an simbox.xyz file generated using packmol. It seems ReaxFF does not need bonds and angles in the data file. I want to generate a data files with just coordinates, please let me know how we can do this. Also can we use ReaxFF force fields with Quartz surfaces.
You can check Paul Norman’s thesis: http://conservancy.umn.edu/handle/11299//93295 I think he did some tests using ReaxFF and alpha-quartz surfaces, through lammps. Surface energies of the (0001) surface, both cleaved and reconstructed, are in fairly good agreement with ab initio data.
Arthur