[lammps-users] Constructing a bead-spring like chain with ellipsoids and springs

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1

Hello LAMMPS users,

I would like to construct (and simulate) a bead-spring chain (like a polymer chain) with beads replaced by ellipsoids and springs connected to the ends of the ellipsoids instead of at their center. From a search of the mail-list archive, I found two possible ways of implementing this in LAMMPS.

  1. By creating rigid bodies by attaching a bead of negligible mass at the ends of the ellipsoids and connecting springs to those beads. But since LAMMPS allows only a limited number of rigid bodies, this doesn’t work for me as I am looking to create multiple chains of this type.

  2. Connecting springs to the center of the ellipsoids and using angle_type dipole to penalize nonzero angle between ellipsoid axis and bond direction. Though for fix nvt/asphere update dipole needed to update dipole direction to coincide with the ellipsoid axis is not implemented.

In the archive, these solutions were suggested more than 5-6 years ago. I am wondering if some features have been added in LAMMPS to facilitate this type of modeling (which unfortunately I have missed to notice) or anyone has been able to find a better approach. Any leads/suggestions would be much appreciated.

Thanks,

Manav

2

There is no limit for the number of rigid bodies in LAMMPS when they are defined via molecule IDs.

Axel

3

Molecule IDs are just an assigned number and have no impact on the structure of the system. So they do not have to coincide with the presence of physical molecules.
In bio-simulations molecule IDs often are assigned per residue, for example.
Axel.

4

Thanks Axel for the suggestion.

From the documentation, it is not clear to me that using molecule ID will work in my case where each molecule consists of multiple rigid bodies and I have many molecules in the system. However, I realized that custom style should work and I have tested that it does.