Hi,
I am trying to simulate and find the persistence length of a bead spring model, which is not going so well. I am wondering if lamms is doing strange things, my energy is a bit off. Energy is nicely conserved, except it sometimes massively spikes. I am also getting fluctuation in my e_pair output. I am using a harmonic potential to connect beads, and an angle style harmonic to make the chain stiff. E_pair should always be 0 correct? For example, from log.lammps. I am not sure if this is a problem.:
33500000 300 0 84.061409 217.30362 -1.068686e-05
33600000 300 0 96.196347 229.43856 1.3172717e-05
33700000 300 0 85.88458 219.12679 -2.9232279e-05
33800000 300 -1.7134004 89.953673 221.48248 -6.9664614e-05
33900000 300 0 83.799358 217.04157 -8.1265138e-05
34000000 300 0 75.640836 208.88304 -1.9692338e-06
34100000 300 0 72.048203 205.29041 1.9413903e-05
I get a spike of -1.7 for some reason. Then it will be 0 for a while. If anyone has calculated the persistence length of a simple bead spring model, I would love to talk. I need to get this nailed down soon so I can continue working on the fun parts of my research. My lammps file is here: