Coarse-Grained Molecular Dynamics Force-Field for Polyacrylamide in Infinite Dilution Derived from Iterative Boltzmann Inversion and MARTINI Force-Field

Abstract

We present a mesoscale model of aqueous polyacrylamide in the infinitely dilute concentration regime, by combining an extant coarse-grained (CG) force-field, MARTINI, and the Iterative Boltzmann Inversion protocol (IBI). MARTINI force-field was used to retain the thermodynamics of solvation of the polymer in water, whereas the structural properties and intrapolymer interactions were optimized by IBI. Atomistic molecular dynamics simulations of polymer in water were performed to benchmark the mesoscale simulations. Our results from the CG model show excellent agreement in structure with the atomistic system. We also studied the dynamical behavior of our CG system by computing the shear viscosity and compared it with the standard IBI model. The viscosity trends of our model were similar to the atomistic system, whereas the standard IBI model was highly dissimilar as expected. In summary, our hybrid CG model sufficiently mimics an infinitely dilute system, and is superior to both MARTINI and IBI in representing the structure and thermodynamics of the atomistic system, respectively. Our hybrid coarse-graining strategy promises applicability in large-scale simulations of polymeric/biological systems where the structure needs to be replicated accurately while preserving the thermodynamics of a smoother surrounding.

pH-Sensitive Co-Adsorption/Release of Doxorubicin and Paclitaxel by Carbon Nanotube, Fullerene, and Graphene Oxide in Combination with N-isopropylacrylamide: A Molecular Dynamics Study

“…These equations are simultaneously solved for short time steps. Besides that, using Equation (3), force can be assigned to the atomic position and time [59,60].…”

“…For calculation of drug diffusion coefficient, mean-square displacement ( MSD ) was calculated; coordinates of atoms are also shown as r while t stands for time. After MSD calculation, using Einstein’s relation (Equation (6)), diffusion coefficient can be calculated for the three-dimensional system [52,53,54,55,56,57,58,59,60,61,62].…”

Engineering the pH-Sensitivity of the Graphene and Carbon Nanotube Based Nanomedicines in Smart Cancer Therapy by Grafting Trimetyl Chitosan

“…Besides, the force is specified to time and the atomic position by using Eq. (3) (42,43). Simple potentials such as the hard-sphere potential can be employed for primary molecular simulation.…”

Chemically specific coarse‐graining of polymers: Methods and prospects

“…194,195 Based on this simplicity, IBI has been used successfully to model diverse polymer systems in both melt and solution state. 43,[196][197][198][199][200][201] The essential premise of IBI is to iteratively adjust parameters describing a specific CG interaction until the probability distribution associated with that interaction is well-matched to that of the HR reference system. After generating reference data for the HR system, this practically involves iteratively (i) performing a CG simulation with a given set of parameters, (ii) comparing computed probability distributions between the CG and HR systems, and (iii) updating CG potential parameters appropriately.…”