Question about the order of the parameters for FENE bond and lj/cut

Hello,

I have a question about bond style fene. Is this the order that the parameters must be placed in the input script for bond_coeff?

bond_coeff K(energy/distance^2) R0(distance) epsilon(energy) sigma(distance) (for the fene bond).

Also, for lj cut/ in the input script, for pair coeff, do I put the parameters in this order?

pair_coeff epsilon(energy) sigma(distance)? (for lj/cut)

Finally, the fene bond potential also includes the lennard jones potential in its formulation, in addition to the nonlinear spring part. Does that mean that atoms that are bonded together will experience two lennard jones potentials, the one that I specified in lj / cut and the one that is automatically specified in the fene bond? Or does the fene bond lennard jones part overwrite the lennard jones specified in lj/cut for atoms that are bonded together? I could not find this answer on the website.

Thank you

Hello,

I have a question about bond style fene. Is this the order that the
parameters must be placed in the input script for bond_coeff?

bond_coeff K(energy/distance^2) R0(distance) epsilon(energy) sigma(distance)
(for the fene bond).

have a look at:
http://lammps.sandia.gov/doc/bond_coeff.html
http://lammps.sandia.gov/doc/bond_fene.html

Also, for lj cut/ in the input script, for pair coeff, do I put the
parameters in this order?

pair_coeff epsilon(energy) sigma(distance)? (for lj/cut)

http://lammps.sandia.gov/doc/pair_coeff.html
http://lammps.sandia.gov/doc/pair_lj.html

Finally, the fene bond potential also includes the lennard jones potential
in its formulation, in addition to the nonlinear spring part. Does that
mean that atoms that are bonded together will experience two lennard jones
potentials, the one that I specified in lj / cut and the one that is
automatically specified in the fene bond? Or does the fene bond lennard

depends on your exclusions settings.

jones part overwrite the lennard jones specified in lj/cut for atoms that
are bonded together? I could not find this answer on the website.

no. see the special_bonds command documentation.

http://lammps.sandia.gov/doc/special_bonds.html

everything you ask about is documented clearly in the lammps manual.
what the lammps manual is not, is a textbook on how to implement
and perform MD simulations. there are a ton of those around.

axel.