Hello Everyone,
Sorry for not explaining my questions clearly in my previous email.
We are designing a new polymer molecule, (for example the monomer is shown in the figure attached).
My question is: is it possible to calculate the mechanical resonance frequency for such a monomer in Lammps?
The resonance I am concerning now is: the tendency of the monomer to oscillate with greater amplitude at some frequencies than at others. Frequencies at which the response amplitude is a relative maximum are known as the system’s resonant frequencies.
At these frequencies, even small periodic driving forces can produce large amplitude oscillations.
Thank you very much,
Lili Zhang
I would think that the resonance modes and frequencies depends
strongly on the length of the polymer. (Unless you are talking about
normal modes of excitation within each monomer.) Also, for a polymer
of a reasonable length, I suspect that the presence of solvent could
damp out out the low-frequency resonance modes to the point that
resonance is difficult to detect. (My impression is that this is a
serious problem with proteins, for example, although people do NMA on
proteins in spite of it.)
I don't know if this helps, but there were some related questions
posted on the lammps mailing list a couple years ago.
http://lammps.sandia.gov/threads/msg03264.html
http://lammps.sandia.gov/threads/msg07835.html
http://lammps.sandia.gov/threads/msg07902.html
Lili,
Hello Everyone,
Sorry for not explaining my questions clearly in my previous email.
We are designing a new polymer molecule, (for example the monomer is shown
in the figure attached).
My question is: is it possible to calculate the mechanical resonance
frequency for such a monomer in Lammps?
This question is by default ill-posed.
The resonance I am concerning now is: the tendency of the monomer to
oscillate with greater amplitude at some frequencies than at others.
Frequencies at which the response amplitude is a relative maximum are known
as the system's resonant frequencies.
At these frequencies, even small periodic driving forces can produce large
amplitude oscillations.
Well, the fact that you cut and paste from Wikipedia tells me that
there is a good chance that you don't know exactly what you need. You
sound like an experimental person thus I would suggest to
explain better what you are after. You are trying to synthesize a
polymer but then you are looking
for a normal mode that will break the monomers apart? Is that in order
to ensure the strength of your polymer? If I understand correctly you
will be looking at those/that normal mode(s) of your polymer that
represent a collective motion of the atoms conforming your monomer and
have a tendency to pull the polymer apart. There might people in the
list better qualified that I am to offer help here.
You could certainly do a normal modes calculation with Lammps but
first, I don't know if any of the available potentials (reactive or
not) represent good parametrizations of your system. Second, in order
to find the normal modes you'll have to compute the Hessian matrix and
currently there is no available routine to do that in Lammps although
you could write your own (not hard).
Hope this helps,
Carlos
Lili,
Carlos and Andrew have made some great points, and I would like to
just add the following:
1) I strongly advice you start with quantum chemical calculations.
Classic potentials with empirical parameters fit to experimental
and/or QC calculated data. Since you claim you are "designing a new
molecule", chances are that there are no good parameters, if not
nothing at all, for your new molecule.
2) Try look through the NIST CCCBDB website for experimental and
calculated "vibrational" data.
Cheers,
Ray