Dear all,
I want to create a data file with UFF force field parameters. Which method do you suggest to generate such a data file?
Regards
Mina
Dear all,
I want to create a data file with UFF force field parameters. Which method do you suggest to generate such a data file?
i would recommend to keep the force field parameters *outside* the
data file and use *_coeff statements instead, possibly in a separate
file to be integrated via the "include" command.
there are tools to build data files. LAMMPS Molecular Dynamics Simulator
but what is the best approach depends very much on the kind and size
and complexity of your system. keep in mind, that force field
calculations require *two* crucial steps: 1) generating the geometry
and bond connectivity (other topological data can be inferred from
that) and 2) assign force field specific atom types to the atoms. UFF
uses a rule based system, IIRC, so possibly you have to apply some
scripting. my personal preference for that is using VMD, but i am very
comfortable with VMD/Tcl scripting and not everybody is.
you probably want to start with something small and simple, where you
can do steps/corrections manually in a text editor before automating
them with scripting.
axel.