Hi LAMMPS users,
I would like to simulate a polymer, where the monomer is a elongated objects made of two or three LJ beads.
Let’s say like this
OO–OO–OO
OOO–OOO–OOO
– represent the springs
OO or OOO represent the monomer

The monomer are rigid, meaning they should be considered as a single entity. I also need to implement both stretching and angle potential similar to bead spring model for polymer chain. But the difference here is stretching potential should act between center of mass of two “monomers” and the angle is defined between the center of mass of the 3 monomers. I plan to use a brownian simulation of such systems.
Can current LAMMPS simulate such a model ? Which source files I need to change to incorporate the model ?

This could probably be done using either fix rigid (on the monomers) or pair style body, where you also put in a specific, otherwise non-interacting particle representing the center of mass.
But there is two caveats.

1. If you have the bond and angle interactions between the center of masses of the rigid bodies, what should the interactions be between the individual neighboring LJ beads?
Normally, when you have a system of connected beads, say A-B-C-D-E, then only beads A and E would have non-bonded interactions unless you change the special_bonds setting (the default is).
For spring-bead polymers (w/o angles!) you typically change the default setting (special_bonds lj/coul 0.0 0.0 0.0) to excluding only the direct neighbors (special_bonds lj/coul 0.0 1.0 1.0) thus you have non-bonded interactions of A with C, D, E, of B with D, E, and of C with A, E. For your geometry this is not as straightforward to implement.

2. With the setup you describe the rigid bodies can freely rotate around the center of mass. So instead of OOO-OOO-OOO you might have

``````O   O
O----O--OOO
O     O
``````

Is this desired?

I needed a monomer made of three beads 000 and it should act like a rigid body.
000–000-000
1-----2------3
So the bending potential should act between the monomers 1-2-3. stretching potential can also act between 1-2 monomers. Probably asphere particles with stretching and bending potentials also work. The criteria here is I need to simulate a polymer with elongated monomers.
This is ambiguous. As I already alluded to, you must pick a reference point for each monomer to link it to the next monomer. This could either be the central particle or one of the outer particles. So for a sequence: `123--456--789` you have to choose where to place the interactions. If you connect the monomers with stretching and bending as via the central particles as `2--5--8`, i.e. have bonds 2-5, 5-8 and angle 2-5-8, you have the uncontrolled rotation. When using ellipsoids, you have the same problem. But you can also use bonds 3-4 and 6-7 and angles 2-3-4, 3-4-5, 5-6-7, 6-7-8 to control stretching and bending. Or some other combinations. Each is a different model and would somehow match your description.
May I suggest looking at the MOLC package, which contains a `bond_style ellipsoids`. It is not (yet) in the official LAMMPS distribution, but you can find it in this fork of the previous release (Jun22).