I do not expect a cut and paste solution. In fact, I am convinced by now
that there are none, having tried for four weeks now.
it is a fundamental principle of research, that the solution is only
then easy to find, if you have understood the problem. obviously, you
have not yet reached that point. my guess is, you are looking at it
from the wrong perspective. you want to solve the entire problem in
one go. that rarely works and only for simple problems. more complex
issues, you have to break down into small sub-problems and then solve
them one at a time.
Regarding the tools, I tried those too. My question was just in case I
missed something, and someone experienced might actually know how do
something like this. I wasn't able to, after reading their documentation and
again, there is a different between more-or-less blindly repeating
something and understanding what it does. simplify your problem and
find a solution for that. it will be easier. then crank up the
complexity. identify where there are patterns and then you can write
programs to follow them and do the tedious work for you.
VMD topo-tools does come with guess functions. But say for 10 chains, 100
polystyrene monomers each, the number is simply too large to even figure out
which of those dihedrals/impropers/angles may be incorrectly defined and
edit them out. So guess functions of topo tools are ruled out.
i disagree. i wrote topotools *exactly* for using it in cases that you
describe. but you can only use them correctly if you understand the
different between the coordinates of a molecule and its topology and
how you can use internal coordinates and a template to describe a
monomer and then generate a polymer from it, using the templated
please also keep in mind, that it is not necessary to generate a
"perfect" initial configuration. there are all kinds of methods that
can be used to build an initial configuration and then relax it into a
proper equilibrated conformation. this is what i mean with "following
a protocol". these *are* described in the literature, you just have to
keep looking and keep reading.
My model is that of polystyrene. I want to model this, as per unified atom
model. As to the choice of force fields, I have some flexibility there, as a
lot of force-fields and their variations can be applied to this system (
Researchers have applied various force-fields) . I intend to apply them
one-by one and see as to which one gives me best results, for the model I
so, but that is an important point, as the force field itself
determines what kind of topology you have to use. remember, you do a
model of the molecule, not the real thing, and models can use
different components and different levels of approximation. this is
what you have to apply when constructing your system.
I have gone through LAMMPS tutorials and samples scripts, and done those
simulations. I have also carried out simulations with bead-spring models of
polymers. There I was able to get results. Those I could generate with
programming. Here, I am unable to figure out, how to go about generating the
model for LAMMPS in the first place.
and i have to repeat, this is all dependent on your problem solving
skills. the tools are all there and there is lots of examples around.
you simply need to identify what are the key steps, and then translate
them to your system. this is no rocket science, but short of doing
your work for you, there is little else that we can do for you.
Could you elaborate on the 'having an understanding of the molecular model'
part? What information do I need to know, other than details of the molecule
I want to model? Specifically, is there something I do not know?
this has already been answered.