@article{a3e6325c44c545bab39711026f319169,
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.",
author = "Mashayak, \{S. Y.\} and Jochum, \{Mara N.\} and Konstantin Koschke and Aluru, \{N. R.\} and Victor R{\"u}hle and Christoph Junghans",
note = "We would like to thank K. Kremer for bringing the authors of this paper together at the Max-Planck-Institute for Polymer Research in Mainz and for his continuous support of this project over the years. SYM and NRA acknowledge financial support by the NSF under grant Nos. 1264282 and 1420882 and AFOSR under grant No. 11157642. CJ was financially supported by SFB 625 in the framework of the multiscale modeling initiative of the Max-Planck Society (M) during his time in Mainz in 2011 and acknowledge hospitality at KITP in July 2012, where this research was supported in part by the National Science Foundation under grant number NSF PHY11-25915. CJ thanks LANL for a Director{\textquoteright}s fellowship and the MPG for hospitality in 2013 at MPI-P. SYM, CJ, and VR acknowledge Shell S. for helpful suggestions during the implementation of the relative entropy method. K. Koschke acknowledges funding by the Nestl{\'e} Research Center. MNJ acknowledges C. Peter for fruitful scientific discussions and the DFG Emmy Noether program for financial support. Assigned: LA-UR-13-26878. LANL is operated by Los Alamos National Security, LLC, for the National Nuclear Security Administration of the U.S. DOE under Contract DE-AC52-06NA25396. 3",
year = "2015",
month = jul,
day = "20",
doi = "10.1371/journal.pone.0131754",
language = "English (US)",
volume = "10",
journal = "PloS one",
issn = "1932-6203",
publisher = "Public Library of Science",
number = "7",
}