- it could probably be adapted to the pizza toolset). However, with a psf
file it is possible to perform analyses with Charmm or VMD (it would be
nice if VMD could read LAMMPS's data file directly - maybe we can put a
feature request to them).
i have looked into extending LAMMPS support in the VMD molfile plugins
not so long ago. the main problem is: LAMMPS is too flexible.
to get all the information that VMD needs, it basically needs the
whole input to LAMMPS (including variables, scripts etc.) which is
not possible. it would be easier to teach LAMMPS writing a matching
.psf file and make it an option to the dcd/xtc/lammps dump output.
i have been thinking about this for a while but was up to now
held back due to teaching and administrative commitments...
there have been repeated discussions amongst 'high-end' VMD users
and developers to come up with a self-describing, flexible, low
memory, compressible, and fast to read file format, but this has
not yet left the planning stage. coming up with a file format that
can be used _efficiently_ for whole range of applications from
very large scale classical MD to quantum chemistry is not an easy task...
To use the dcd format,
dump positions dcd atom 100 filename.dcd
To use the xtc format:
dump positions xtc atom 100 filename.xtc [precision]
where precision can be specified - a value of 100 means that coordinates
are stored to 1/100 nanometer accuracy.
Incidentally, for Steve and Paul and others at Sandia, would it be
possible to add a community wiki to the LAMMPS website where the
collective LAMMPS community can contribute their knowledge and scripts
that they've developed while using LAMMPS?
in case setting up and running a wiki would be too much overhead,
there are a number of alternatives, e.g.:
- for VMD we use the BioCoRE framework to communicate larger files
and for chats (one can create public projects, so that everybody
- google groups offers wiki-like webpages and (small) file uploads.
we are using that for CP2K.