title: Relative Entropy and Optimization-Driven Coarse-Graining Methods in VOTCA.
abstract: We discuss recent advances of the VOTCA package for systematic coarse-graining. Two methods have been implemented, namely the downhill simplex optimization and the relative entropy minimization. We illustrate the new methods by coarse-graining SPC/E bulk water and more complex water-methanol mixture systems. The CG potentials obtained from both methods are then evaluated by comparing the pair distributions from the coarse-grained to the reference atomistic simulations. In addition to the newly implemented methods, we have also added a parallel analysis framework to improve the computational efficiency of the coarse-graining process.
authors.affiliation: Department of Mechanical Science and Engineering, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, United States of America.
authors.forename: S Y
authors.initials: SY
authors.lastname: Mashayak
authors.affiliation: Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany.
authors.forename: Mara N
authors.initials: MN
authors.lastname: Jochum
authors.affiliation: Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany.
authors.forename: Konstantin
authors.initials: K
authors.lastname: Koschke
authors.affiliation: Department of Mechanical Science and Engineering, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, United States of America.
authors.forename: N R
authors.initials: NR
authors.lastname: Aluru
authors.affiliation: Department of Chemistry, University of Cambridge, Cambridge, United Kingdom.
authors.forename: Victor
authors.initials: V
authors.lastname: Rühle
authors.affiliation: Computer, Computational, and Statistical Sciences Division, Los Alamos National Laboratory, Los Alamos, NM 87545, United States of America.
authors.forename: Christoph
authors.initials: C
authors.lastname: Junghans
mesh_terms: D000465:Algorithms; D019277:Entropy; D000432:Methanol / Q000737:chemistry; D008968:Molecular Conformation; D056004:Molecular Dynamics Simulation; D013997:Time Factors; D014867:Water / Q000737:chemistry
chemical_list: D014867:Water; D000432:Methanol