Dear LAMMPS users,
I am trying to perform a dissipative particle dynamics (DPD) simulation of a bunch of polymer chains diffusing in free solvent. The objective is to determine the mean-square radius of gyration and mean-square displacement of the chains’ center-of-mass. Some details of my simulation are as follows:
· Cubic simulation box of side length 10 and periodic BCs in all 3 directions
· Total number of beads = 3000
· Two types of beads: polymer and solvent beads. There are a total of 300 polymer beads (30 chains of 10 beads each) and the remaining beads are solvent particles.
· Bead spring model for the polymer chains with harmonic spring
· Time integration using the standard velocity verlet algorithm
· Initially, all the beads are frozen and the system attains the target temperature of 1.0 after running for some time.
The problem I am facing is that I always get an error message saying that certain bond atoms are missing on a particular processor at a certain time-step. I have tried to increase the skin distance in the neighbour command but this merely results in the simulation running for a longer time before this error message appears. I have read on this mailing list that this error could be caused by bad dynamics but I doubt that this is the issue in my case as my parameter settings (aij values of 25 for DPD conservative force, equilibrium bond length of 0.7, and a spring force constant of 40) appear to be commonly used in DPD studies on polymers. I am performing standard DPD without using the segmental repulsive potential for the time being.
I have attached my input script and data file. I am using the LAMMPS version released on 16 Feb 2016.
Thanks.
Best,
Karthik.
test.dat (173 KB)
test.in (729 Bytes)