Angles for Coarse-Grained Red Blood Cell

LAMMPS LAMMPS General Discussion
1

no_lbm_eneg3.lmp (6.1 KB)
Hello,

My research group is attempting to create a coarse grain model of Red Blood Cells in a similar fashion to an approach outlined in the following paper: A parallel fluid-solid coupling model using LAMMPS and Palabos based on the immersed boundary method - PMC

We are stuck defining the angles for the system. We have developed a python script to write a data file for the simulation, in which the positions of the particles that from the cell are arranged in a hollow sphere. If any two particles are within a certain distance from each other, a bond is added between those two particles. Similarly, if any particle is adjacent to those bonds, it is checked to potentially form an angle. The script works and produces the positions, bonds and angles for the system. However, whenever any angle energy is added to the system, the simulation crashes. One thing we tried was to place a restriction on the angles so that only angles close to the equilibrium angle were defined, although that did not stop the simulation from crashing. I have uploaded the script for the data file as well as the LAMMPS input file.

Any ideas on why the simulation is crashing and how to fix it would be greatly appreciated!

Cell_Creation.py (16.0 KB)

no_lbm_eneg3.lmp (6.1 KB)

2

Try dumping information about angles (atoms involved, energy, and the value of the angle) from LAMMPS by using fix property/local, compute angle/local, and dump local.
You’ll see that some angles are equal to nan because you have overlapping atoms.
Cool project, BTW. :slight_smile:

3

Thank you for the response.

I have done as you suggested and all of the angles are NaN. Do you have any idea what might be causing this to occur? I know it is a general question, but I am quite confused. Is there any precedent for this to happen?

4

As I said you have overlapping atoms, i.e. at least two atoms which have exactly the same coordinates. When such atoms are a part of the same angle, NaN occurs.