How to set the boundary force-field parameters of the periodic box of natural rubber

Hi,
I construct the periodic molecular model of natural rubber in Accelrys Materials Studio (MS), there are some segments out of the MS box due to the great length of the natural rubber molecule. I know that the tool “msi2lmp.exe” could translate the MS molecular model into the datafile which can be read in LAMMPS, and the translation work is successfully carried out. However, now, the first problem I confront is that I am not sure whether all the atom informations of MS box, especally the rubber segments out of the MS box, are translated into the box in the LAMMPS datafile. The second problem, the most important, is that I don’t know how in LAMMPS to set the force field parameters of bond, angel and dihedral angle at the periodic boundary of the polymer box, because the rubber molecular is too complex. Would you tell me the rules in LAMMPS‘ COMPUTATION about dealing with the boundary molecules of complex polymer in the LAMMPS’ BOX. And, what should I do next? Would you give me some help. Than you very much.
Best wishes !

D. Chai

Hi,
     I construct the periodic molecular model of natural rubber in Accelrys
Materials Studio (MS), there are some segments out of the MS box due to the
great length of the natural rubber molecule. I know that the tool
"msi2lmp.exe" could translate the MS molecular model into the datafile which
can be read in LAMMPS, and the translation work is successfully carried out.
However, now, the first problem I confront is that I am not sure whether
all the atom informations of MS box, especally the rubber segments out of
the MS box, are translated into the box in the LAMMPS datafile.

have a look at the data file and your source files and compare the
number of atoms.
also, use a visualization software to check. if you still have doubts,
i would suggest to create a very simple test molecule with only a few
atoms, but the same concerns and manually compare each atom, bond,
angle, and so on.

The second
problem, the most important, is that I don't know how in LAMMPS to set the
force field parameters of bond, angel and dihedral angle at the periodic
boundary of the polymer box, because the rubber molecular is too complex.

why should the parameters at the periodic boundary be different from
the ones elsewhere?

Would you tell me the rules in LAMMPS‘ COMPUTATION about dealing with the
boundary molecules of complex polymer in the LAMMPS' BOX. And, what should I
do next? Would you give me some help. Than you very much.

how LAMMPS handles things specifically is explained in the manual,
which assumes that you have sufficient basic knowledge of MD. it is
near impossible to summarize this in a few sentences in an e-mail,
especially not knowing what your level of experience is. perhaps you
should consult with your adviser or colleagues with more experience in
MD.

axel.

If your box is periodic, then when LAMMPS reads a data
file it will wrap any atom back into the periodic box
if needed. Regardelss, it will throw an error if it loses an atom

in the process, which should not happen for a periodic
box.

Steve

Dear Axel and Steve,
Your comments and advices are appreciated. My model has been constructed. It is true that the simple test is very useful way to help ourselves to examine the errors or ideas.

D. Chai