In present day the crux of performing coarse-grained simulations is the actual parameterization of the (molecular) interactions and the validation of the outcome of a simulation. In a recent effort we have work on the former and have devised a data-driven scheme, termed Automated Fragmentation and Parameterization (AFP), that uses Monte Carlo based fragmentation techniques in combination with excluded volume and free energy information of molecular pairs to obtain robust coarse-grained parameter sets. We tested AFP on a database of over 5000 molecules by computing the wet octanol/water partitioning . More recently, we extended AFP and computed diffusion coefficients of over 11000 molecules in aqueous solution . In this presentation we will give an overview of the AFP method, highlighted by a number of recent industrial applications.  Fraaije et al., Coarse-Grained Models for Automated Fragmentation and Parametrization of Molecular Databases, J. Chem. Inf. Model. 2016, 56, pp. 2361–2377.  Fraaije et al., Calculation of Diffusion Coefficients through Coarse-Grained Simulations Using the Automated-Fragmentation-Parametrization Method and the Recovery of Wilke–Chang Statistical Correlation, J. Chem. Theory Comput., Articles ASAP (2017).
Journal: TechConnect Briefs
Volume: 4, Informatics, Electronics and Microsystems: TechConnect Briefs 2018
Published: May 13, 2018
Pages: 5 - 8
Industry sectors: Advanced Materials & Manufacturing | Sensors, MEMS, Electronics
Topics: Informatics, Modeling & Simulation