Dear lammps users,
I am a new user of Lammps. I would like to model Inorganic fullerene nanoparticle (MoS2). The information which must be included in simulations contains bonds, angles, dihedral angles, etc.
How can it be possible to create lammps input file using information contained, for example, in .pdb (coordinates) and .psf (bonds, angles, etc.) files?
Thank you,
Evgeniya
See the tools/ch2lmp tool, which converts PDB files into LAMMPS data files.
Steve
See the tools/ch2lmp tool, which converts PDB files into LAMMPS data files.
i don't think that this will work, since this script also needs a
matching set of charmm compatible topology and parameter files and
those don't tend to be available for inorganic materials.
creating the data file is possible with other means, see.
http://lammps.sandia.gov/prepost.html
axel.
Dear Axel and Steve,
Thank you very much for your reply.
Best regards,
Evgeniya
I would recommend using topotools. VMD can understand the topology
and coordinates in PSF and PDB files, and Axel's topotools can convert
them into LAMMPS data format.
Some crude instructions to follow:
-You can open a PSF file using VMD. ("vmd monster.psf")
-Then right click on that file (eg "monster") in the white box in the
middle of the "VMD Main" window, and select "Load Coordinates into
Molecule" pull-down menu option.
-Browse for your PDB file and load it. (After you have loaded the pdb
file, you should see the molecule displayed in the graphics window.)
-Select "Extensions"->"Tk Console" and use the topotools commands to
convert this molecule into a lammps DATA file. They are discussed
here:
https://sites.google.com/site/akohlmey/software/topotools/topotools-tutorial---introduction
Cheers!
Andrew