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

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 represent...

Authors:   Pallavi Banerjee; Sudip Roy; Nitish Nair
Journal:   Journal of Physical Chemistry B
Year:   2018
DOI:   10.1021/acs.jpcb.7b09019
Publication date:   18-Jan-2018
Facts, background information, dossiers
  • Martini
  • water
  • molecular dynamics
  • shear viscosity
  • molecular dynamics…
  • Inversion
  • interactions
  • dilution
  • concentration
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