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espressomd / espresso

The ESPResSo package
https://espressomd.org
GNU General Public License v3.0
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FENE bonds breaking during the simulation #3605

Closed dpo854 closed 4 years ago

dpo854 commented 4 years ago

What is the default equilibrium bond length for FENE? Is it 1 or zero in distance units? Is it the reason polymer bonds often break during the simulation?

KaiSzuttor commented 4 years ago

The default for r_0 is 0.0. That may or may not be the source of your issue. Please provide a minimal not working example.

dpo854 commented 4 years ago

I see. But then how do you prevent two adjacent bonded particles from collapsing into each other? Does the non-boned potential act between two bonded particles?

KaiSzuttor commented 4 years ago

Does the non-boned potential act between two bonded particles?

yes

fweik commented 4 years ago

In a typical (Kermer-Grest type) polymer model, you have the r_0 of the bond at zero, but Lennard-Jones (LJ) interactions between the bonds, which keeps them at 1 sigma at equilibrium. This is also stable at unit temperature. You can have a look at samples/minimal-polymer.py for a minimal setup, this uses a purely repulsive LJ (=WCA), but this also works with an LJ that has an attractive part.

If you don't have a repulsive interaction between the beads, and don't want them so sit on top of each other, you have to set a non-zero r_0.