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[lammps-users] Simulation of polymer migration in cavities
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[lammps-users] Simulation of polymer migration in cavities

From: Nagarajan Karthik <a0108483@...6748...>
Date: Tue, 20 Jun 2017 12:45:38 +0000

Dear all,


I wish to perform a Dissipative Particle Dynamics simulation of polymer chains migrating in an array of cavities in the presence of a steady external field. To do this, I am using a cubic simulation box of side length 20 with periodic boundary conditions in all 3 directions. There are 3 types of particles in the simulation. The solid mass comprises of 8818 particles arranged to form a spherical cavity. Also, there are 30 polymer chains with 10 beads each and 12481 solvent beads.  Please find attached the LAMMPS input script (‘ and data file (‘input_lam.dat’). When this simulation is run for more than 20 million time-steps with dt = 0.04, the component of the end-to-end vector of some chains along the direction of the field suddenly becomes very large (of the order of 10^4) at certain time-steps before returning to normal. I have attached a graph showing the variation in end-to-end vector of two chains (chains 14 and 24) with time. I am using chains with harmonic bonds. The force constant is 40 and the equilibrium bond length is 0.7. The problem does not arise in the absence of the external force.


I would appreciate if someone could clarify the following issues:


1.       What could be the cause of this problem? I have checked the values of various thermodynamic parameters (temperature, pressure etc) and nothing seems amiss. Also, why didn’t the simulation stop with a ‘Bond/Angle atom missing on proc ‘ error message when the chains became abnormally large?


2.       What can be done to rectify this problem?











Attachment: input_lam.dat
Description: input_lam.dat

Attachment: End-to-End Vector.jpg
Description: End-to-End Vector.jpg