Very newbie question this as I've only just started experimenting with LAMMPS.
To avoid me having to code them from scratch, are there LAMMPS molecule file / data file definitions for common molecules (e.g. CO2, PF6, Imidazole, BMIM) available online (or a public domain program that can generate the definitions for given molecules)?
Thanks
Tony
Very newbie question this as I've only just started experimenting with LAMMPS.
To avoid me having to code them from scratch, are there LAMMPS molecule file / data file definitions for common molecules (e.g. CO2, PF6, Imidazole, BMIM) available online (or a public domain program that can generate the definitions for given molecules)?
no.
but there isn't so much to it and it actually is a good way to learn
about the kind of information that LAMMPS needs by coding them
yourself.
please note, that in most cases, people do _not_ use molecule files at
all, but rather prepare complete data files using pre-/postprocessing
(e.g. moltemplate, or packmol or topotools or custom scripts or a
combination of those). again, since the data file format is documented
in great detail (if anything it may be too detailed), it is good
practice to learn how to do these files from scratch with a few rather
simple examples. it will help you enormously later on, in case you
need to debug some automatically created data files. keep in mind,
that even the best tools may have bugs... (i've written one of those
and i am regularly shocked about what kind of bugs occasionally
surface).
axel.
I’m happy to add new molecule examples to moltemplate if you want to share any that you have built. (There are a few OPLS examples here).
Currently the tricky part is figuring out the correct atom type for the atoms in your molecule (by reading the “oplsaa.lt” file).
Andrew
(I’m about to spam the mailing list to ask for help to make more forcefields available.)
To avoid me having to code them from scratch, are there LAMMPS molecule
file / data file definitions for common molecules (e.g. CO2, PF6, Imidazole,
BMIM) available online (or a public domain program that can generate the
definitions for given molecules)?
There is now:
Did you notice the Tom Lee's recent post to the mailing list? (I
finally did.) For more details, see:
http://lammps.sandia.gov/threads/msg66441.html
cheers
andrew