Dear ALL,

I don’t know how to use the special_bonds command? If I do Langevin simulation of polymer with coarse-gained bead spring model and FENE bond potential. How can I give the special_bonds numeric coefficients ? What is the difference of special_bonds 0.0 1.0 0.0, special_bonds 0.0 1.0 1.0, and special_bonds 1.0 1.0 1.0? And, how can I choose them? Could some experts give me any suggestion?

hi steve and all,

I want to use the following potential:

e (ij) = A/r + Bexp(-Cr) - D(sigma/r)^^12 - E(sigma/r)^^6

to model the two types atom interaction.

where r (rij) is the distance between atom i and j. A,B, C,D is constant.

I am aware that the long range potential should use the Ewald summation. I was wondering that how to achieve the mixed potential? Do I need to write the code myself? or Lammps already has all these seperated potential terms. If that, where can I start? If someone had similar experience, please give me some suggestions. I’ d appreicate that.

Thanks

AC

If you understand what 1-2, 1-3, and 1-4 interactions are in a molecule
with bonds, then special_bonds will make sense. For a linear FENE
chain, just number the beads in the chain from 1 to N. The 1-3 partners
are beads (1,3), (2,4), (3,5), etc. Pairwise (LJ) interactions between
those pairs will be turned off if the 2nd special_bonds coeff (1-3) is 0,
otherwise they will be turned on partially or fully.

Steve

Not sure what you mean by two types and "mixed". But if
you just want the potential in your formula, then I suppose
you could use pair hybrid/overlay with a sub-styles coul (A term),
lj/cut (D and E terms) and buck (B and E terms, but set the 1/r6 coeff
to 0).

Or you could just take pieces of those 3 files and create your
own new pair_style spiff.

Steve

Thanks Steve and AEI for kind reply. In the special_bonds doc page: http://lammps.sandia.gov/doc/special_bonds.html

you can read that" For a lj units system with FENE bonds a setting of special bonds 0 1 1 should be used. ". I can’t understand why we must turn on the 1-3, and 1-4 interactions and turn off the 1-2 interaction.

Thanks.

wende

2008/9/15 Steve Plimpton <[email protected]>

That's the typical FENE bead-spring model when you don't have angle
or dihedral terms in your chain.

Steve