I want to import a pdb file as a data file to LAMMPS. As much as I know, for this aim first I have to create a psf file from pdb file and then use charmm2lammps tool (useing charmm ff) to make .in and .data files. Is this the actual way to do import a pdb file to LAMMPS?
I want to import a pdb file as a data file to LAMMPS. As much as I know, for
this aim first I have to create a psf file from pdb file and then use
charmm2lammps tool (useing charmm ff) to make .in and .data files. Is this
the actual way to do import a pdb file to LAMMPS?
no. lammps doesn't do any system preparation. you have to do this
with other tools.
the question is not a question about the file format, but rather what
would be _in_ this file and whether it would match the physics of the
system that you want to study.
in principle it is possible to load a .pdb file into VMD and write out
a .data file that would contain those coordinates, but to make that
a meaningful input, you need to assign force field types and add
the corresponding parameters. for bio molecules, you can use the
tools from CHARMM or NAMD to build the .psf/.pdb file combo
and then convert it with the help of the corresponding force field
data base and parameter files to LAMMPS input. for anything else,
you would have to script/program/imagine it yourself.
cheers,
axel.
yes - that is the correct procedure - i.e. to use a pre-processing
tool like charmm2lmp to prepare the LAMMPS input files
Steve