I have a doubt regarding the generation of a polymer like PVC in lammps.
If i want to do the polymer generation using an all atom approach and not a united atom one,
then how do i specify in the def.chain file that i have a monomer consisting of two atom types( -CH2- and -CHCl )??
or do i HAVE to use it by taking 1 monomer itself as a bead ? (united atom)
thanks in advance,
def.chain tool provided by LAMMPS is suitable for generating bead-spring
polymer chains for united atom and coarse-grained simulations. In order
to generate an all-atom system i suggest that use Topotools. For that
you need a topology file, such as a pdb file, from each component of
your system, you can easily create them using for instance Avogadro
I personally use Packmol tool
(http://www.ime.unicamp.br/~martinez/packmol/) to generate my systems
configuration, and then use Topotools to generate Lammps data file.
I hope it helped.