I was wondering what the best way to handle a simulation where say I wanted to use Class2 to model a polymer surface and Charmm to model a peptide in solution that is in contact with a Class2 surface. Obviously there is the issue of cross terms for the pair wise forcefield but I have a solution for that. What I am wondering about is how to handle the special bonds in the system. As I understand it there is no way to use say special_bonds charmm for a certain part of the system and then another special_bonds style for another type. Is there a work around that has been developed for this type of simulation? Or for example if I was modelling a peptide in solution (CHARMM) in contact with a gold substrate (EAM), in this case if I understand the manual correctly then no special bonds would be used anywhere in the system.
Class2 + CHARMM is a hard one. There is no current way to have
2 sets of special_bond params, each for a subset of the system.
For CHARMM + EAM it is not an issue. EAM ignores the special
bond settings. So set them to CHARMM values. Assuming you
put no hard-wired bonds between EAM atoms, then the EAM part will
compute normally with pair hybrid.
--- assumptions ---
I assume you have two polymers with no bonds connecting them. One
polymer uses only charmm force-field conventions. The other uses only
the class2 conventions.
For the class2 polymer, I assume you want to use something like this:
special_bonds 0 0 1
And for the charmm polymer, I assume you want to use this:
special_bonds 0 0 0
--- would this work? ---
To mix this polymer with a polymer using different special_bonds
rules, you could turn ALL 1-3 and 1-4 pairwise interactions ON using:
special_bonds 0 1 1
...and then manually add additional tabular bonds between every pair
of 1-3 atoms and 1-4 atoms whose forces exactly cancel the
interactions you were trying to exclude earlier (using "special_bonds
0 0 0" or "special_bonds 0 0 1").
To do this, you can use tabular bonds to customize the force
between any pair of atoms. http://lammps.sandia.gov/doc/bond_table.html
(Use something like "bond_style hybrid table spline 1000 class2 ...")
In this example you would need to cancel out the 1-3 pairwise
interactions between for every triplet of adjacently bonded atoms.
You would also need to cancel out the 1-4 interactions for every
quartet of adjacently bonded atoms ...UNLESS the two atoms belong to
the class2 polymer.)
I don't know if this solves your problem, but it requires some extra
work on your part.
Good luck.
Andrew
(As Axel pointed out in an earlier email, adding extra bonds to your
system will change the list of atoms which LAMMPS internally considers
to be 1-3 and 1-4 atom pairs. However since we are using "special
bonds 0 1 1", it should not matter.)