thanks Axel for your quick reply,
as another question, does VMD (that is, topotools plugin you have written) generate data file of lammps code?
i have previously made the data file of lammps program for polymer molecules myself, but in the case of clay materials, it is difficult to define the Dihedrals correctly.
kind regards
mohammadhasan
thanks Axel for your quick reply,
as another question, does VMD (that is, topotools plugin you have
written) generate data file of lammps code?
the up-to-date topotools documentation is here:
http://sites.google.com/site/akohlmey/software/topotools/topotools---documentation
i have previously made the data file of lammps program for polymer
molecules myself, but in the case of clay materials, it is difficult
to define the Dihedrals correctly.
where is the difficulty?
topotools only provides an abstraction of the low level
VMD tools and a selection of convenience tools written
on top of those. so it is not an automated tool, it
just makes writing scripts to build topologies easier.
some of the simpler ways of using it are highlighted
in the existing tutorials, but those are just the
tip of the iceberg.
as such it is bound by limitations of VMD scripting
and how VMD "sees" molecular data sets. the biggest
issue in this respect are bonded interactions that
straddle periodic boundaries (they *can* be defined,
but require explicit scripting) and assignment of
force field parameters. The former is something that
needs better support in the low level commands, the
latter cannot be solved in all generality, since
different force fields have different strategies
of assigning parameters. i am including a simple
example for a coarse grain force field.
axel.