Paper Citing NAMD - Abstract
Gautieri, Alfonso; Vesentini, Simone; Redaelli, Alberto
How to predict diffusion of medium-sized molecules in polymer matrices. From atomistic to coarse grain simulations
JOURNAL OF MOLECULAR MODELING, 16:1845-1851, DEC 2010
The normal diffusion regime of many small and medium-sized molecules occurs on a time scale that is too long to be studied by atomistic simulations. Coarse-grained (CG) molecular simulations allow to investigate length and time scales that are orders of magnitude larger compared to classical molecular dynamics simulations, hence providing a valuable approach to span time and length scales where normal diffusion occurs. Here we develop a novel multi-scale method for the prediction of diffusivity in polymer matrices which combines classical and CG molecular simulations. We applied an atomistic-based method in order to parameterize the CG MARTINI force field, providing an extension for the study of diffusion behavior of penetrant molecules in polymer matrices. As a case study, we found the parameters for benzene (as medium sized penetrant molecule whose diffusivity cannot be determined through atomistic models) and Poly (vinyl alcohol) (PVA) as polymer matrix. We validated our extended MARTINI force field determining the self diffusion coefficient of benzene (2.27 center dot 10(-9) m(2) s(-1)) and the diffusion coefficient of benzene in PVA (0.263 center dot 10(-12) m(2) s(-1)). The obtained diffusion coefficients are in remarkable agreement with experimental data (2.20 center dot 10(-9) m(2) s(-1) and 0.25 center dot 10(-12) m(2) s(-1), respectively). We believe that this method can extend the application range of computational modeling, providing modeling tools to study the diffusion of larger molecules and complex polymeric materials.
