Skip to main content
U.S. flag

An official website of the United States government

Official websites use .gov
A .gov website belongs to an official government organization in the United States.

Secure .gov websites use HTTPS
A lock ( ) or https:// means you’ve safely connected to the .gov website. Share sensitive information only on official, secure websites.

Dynamically consistent coarse-grain simulation model of chemically specific polymer melts via friction parameterization



Lilian Johnson, Frederick R. Phelan Jr.


Coarse-grained (CG) models of polymers involve grouping many atoms in an all-atom (AA) representation into single sites to reduce computational effort yet retain the hierarchy of length and time scales inherent to macromolecules. Parameterization of such models is often via "bottom-up" methods, which preserve chemical-specificity, but suffer from artificially accelerated dynamics with respect to the AA model from which they were derived. Here, we study the combination of a bottom-up CG model with a dissipative potential as a means to obtain a chemically specific and dynamically correct model. We generate the conservative part of the force-field using the iterative Boltzmann inversion (IBI) method which seeks to recover the AA structure. This is augmented with the dissipative Langevin thermostat which introduces a single parameterizable friction factor to correct the unphysically fast dynamics of the IBI-generated force-field. We study this approach for linear polystyrene oligomer melts for three separate systems with 11, 21, and 41 monomers per chain and a mapping of one monomer per CG site. To parameterize the friction factor, target values are extracted from the AA dynamics using translational monomer diffusion, translational chain diffusion, and rotational chain motion to test the consistency of the parameterization across different modes of motion. We find that the value of friction parameter needed to bring the CG dynamics in line with AA target values varies based on the mode of parametrization with short-time monomer translational dynamics requiring the highest values, long-time chain translational dynamics requiring the lowest values, and rotational dynamics falling in between. The friction ranges most widely for the shortest chains and the span narrows with increasing chain length. For longer chains, a practical working value of the friction parameter may be derived from the rotational dynamics, owing to the contribution of multiple relaxation modes to chain rotation and a lack of sensitivity of the translational dynamics at these intermediate levels of friction. A study of equilibrium chain structure reveals that all chains studied are non-Gaussian. However, longer chains better approximate ideal chain dimensions than more rod-like shorter chains and thus are most closely described by a single friction parameter. We also find that the separability of the conservative and dissipative potentials is preserved.
The Journal of Chemical Physics


molecular dynamics, coarse-grained modeling, polymer dynamics, polystyrene, iterative Boltzmann inversion, Langevin dynamics


Johnson, L. and Phelan Jr., F. (2021), Dynamically consistent coarse-grain simulation model of chemically specific polymer melts via friction parameterization, The Journal of Chemical Physics, [online],, (Accessed May 24, 2024)


If you have any questions about this publication or are having problems accessing it, please contact

Created February 24, 2021, Updated February 26, 2023