I want to model a polystyrene melt, using united atom model. How should I generate that? Where should I be looking for methods to generate that? After creating, I shall be modelling it in LAMMPS, using an appropriate force field.
NIT Trichy
I want to model a polystyrene melt, using united atom model. How should I
generate that?
Where should I be looking for methods to generate that?
start reading here: http://lammps.sandia.gov/prepost.html and continue
with reading publications that did the same or something similar.
there usually is not a "just-do-this-one-magic-command" solution but
some kind of protocol, i.e. sequence of steps, required to set up
anything but ideal crystals or isolated molecules.
axel.
I did go through that page. I also tried searching for publications which did this. However, as you are aware, authors present papers about findings, not the exact process. I came across sentences like “An initial configuration for LAMMPS consisting of 80 monomer units was generated”. I was unable to find how they did it, and hence came to this mailing list, to seek help on how to. Any ideas would be helpful. What I am asking is, how does one go about such a problem, in general? Since creating initial configuration is a pre-requisite for anything other than crystal structures, I am sure many people have problem in this (As can be seen on the large no of questions on this topic).
My problem is, when one wants to perform MD simulations on polymers in LAMMPS, for united atom-models of polymers (specifically polystyrene in this case) how does one go about generating initial structure? For bead-spring models, a Random walk code will do. Say we want to model Polystyrene with a united ‘C-H’ group, yet we do not want just a sphere to represent whole of polystyrene monomer unit, what modelling tools/programming tools will help me?
I am aware of tools given on the http://lammps.sandia.gov/prepost.html page. In those, I was unable to model this (Haven’t yet tried moltemplate).
On the mailing list, for questions about initial structure generation, one advice often given is - “most users write their own code to this”. I want to know if
a) The above tools can model this (whether it is a known fact that they are capable of doing this) and if not
b) How does one go about a programming solution to this problem? I have fair knowledge in C/C++. So if there are specific methods to do this, I can try and understand them.
Brahm Prakash Mishra
NIT Trichy
I did go through that page. I also tried searching for publications which
did this. However, as you are aware, authors present papers about findings,
not the exact process. I came across sentences like "An initial
configuration for LAMMPS consisting of 80 monomer units was generated". I
was unable to find how they did it, and hence came to this mailing list, to
seek help on how to. Any ideas would be helpful. What I am asking is, how
does one go about such a problem, in general? Since creating initial
configuration is a pre-requisite for anything other than crystal
structures, I am sure many people have problem in this (As can be seen on
the large no of questions on this topic).
My problem is, when one wants to perform MD simulations on
polymers in LAMMPS, for united atom-models of polymers (specifically
polystyrene in this case) how does one go about generating initial
structure? For bead-spring models, a Random walk code will do. Say we want
to model Polystyrene with a united 'C-H' group, yet we do not want just a
sphere to represent whole of polystyrene monomer unit, what modelling
tools/programming tools will help me?
I am aware of tools given on the
http://lammps.sandia.gov/prepost.html page. In those, I was unable to
model this (Haven't yet tried moltemplate).
On the mailing list, for questions about initial structure
generation, one advice often given is - "most users write their own code to
this".
Yes. This is right.!!
I want to know if
a) The above tools can model this (whether it is a known fact that they
are capable of doing this) and if not
b) How does one go about a programming solution to this problem? I have
fair knowledge in C/C++. So if there are specific methods to do this, I can
try and understand them.
Merely having the solution of C/C++ is not sufficient. What you should have
is the complete understanding of the model you want to simulate. Ex- for
real crystals, the atom coordinates. Once you have a thorough understanding
of the same, you are on with C/C++ to write your code to generate the
co-ordinates.
Sagar
I did go through that page. I also tried searching for publications which
did this. However, as you are aware, authors present papers about findings,
not the exact process. I came across sentences like "An initial
configuration for LAMMPS consisting of 80 monomer units was generated". I
was unable to find how they did it, and hence came to this mailing list, to
construct a monomer and replicate it. how else?
seek help on how to. Any ideas would be helpful. What I am asking is, how
does one go about such a problem, in general? Since creating initial
there is not *the* way. full stop.
configuration is a pre-requisite for anything other than crystal structures,
I am sure many people have problem in this (As can be seen on the large no
of questions on this topic).
mostly this happens because of people jumping ahead to trying to do
simulations before they understand how their respective model and
force field work and what actually happens in the simulation program.
My problem is, when one wants to perform MD simulations on
polymers in LAMMPS, for united atom-models of polymers (specifically
polystyrene in this case) how does one go about generating initial
structure? For bead-spring models, a Random walk code will do. Say we want
to model Polystyrene with a united 'C-H' group, yet we do not want just a
sphere to represent whole of polystyrene monomer unit, what modelling
tools/programming tools will help me?
I am aware of tools given on the
http://lammps.sandia.gov/prepost.html page. In those, I was unable to model
this (Haven't yet tried moltemplate).
On the mailing list, for questions about initial structure
generation, one advice often given is - "most users write their own code to
this". I want to know if
a) The above tools can model this (whether it is a known fact that they are
capable of doing this) and if not
the documentation of those tools states what they are capable of and
what not. whether this is sufficient for your needs, only you can
tell.
b) How does one go about a programming solution to this problem? I have fair
knowledge in C/C++. So if there are specific methods to do this, I can try
and understand them.
it is not so much the knowledge of a programming language that
matters, but an understanding of which information needs to be
conveyed in which way to the simulation program that matters. see my
comment from above.
both, moltemplate and topotools come with examples showing how to use
them. of course, if you expect to have a cut-n-paste solution for your
specific problem, you will not likely find it. this is where the
understanding of the model comes into play. what tools like
moltemplate and topotools offer are abstractions of the low-level
operations, which are often tedious and error-prone; they are no
replacement for understanding the model. if this was possible, it
would have been programmed.
axel.