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.

Assembly of nothing: equilibrium fluids with designed structured porosity

“…The behavior of the resulting potential was robust with respect to increasing the box size. IBI calculations were performed using the the Versatile Object-oriented Toolkit for Coarsegraining Applications (VOTCA) [24,25], which interfaces with the GROMACS 4.6.5 molecular dynamics (MD) package [20,21].…”

ESPResSo++ 2.0: Advanced methods for multiscale molecular simulation

“…This is also true of LAMMPS input files. Because of the variety of file formats that are supported by ESPResSo++, the integration with existing packages is very easy, for example, VOTCA 1.3 [11] package can cooperate with ESPResSo++ out-of-the-box.…”

“…Molecular simulation methods [1,2,3,4,5,6,7,8,9] have facilitated the study, exploration and co-design [10] of diverse materials. The functional and dynamic properties of biological and non-biological materials at diverse length and time scales can be simulated with sequential coarse-graining methods [1,11] or with concurrent coarsegraining and atomistic methods [12,13]. Such multiscale methods often involve coarsegraining the atomistic degrees of freedom into effective degrees of freedom representing a collection of atoms, entire monomers or even molecules [1].…”

Sequence transferable coarse-grained model of amphiphilic copolymers

“…We thank Burkhard Dünweg and Carlos M. Marques for countless interesting discussions and Tiago E. de Oliveira for the help with the C−IBI scripts implemented in the VOTCA package [36] and all atom force field. We further acknowledge Joseph Rudzinski, Nancy Carolina Forero-Martinez, and Torsten Stühn for critical reading of the manuscript.…”