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This is a collection of coarse-graining tutorials using the VOTCA package. Further information on VOTCA can be found at http://www.votca.org The development of VOTCA is mainly funded by academic research grants. If you use this package, please cite the VOTCA papers: * Versatile Object-oriented Toolkit for Coarse-graining Applications, V.Ruehle, C. Junghans, A. Lukyanov, K. Kremer, D. Andrienko, J. Chem. Theo. Comp. 5 (12), 3211 (2009) * Hybrid approaches to coarse-graining using the VOTCA package: liquid hexane, V. Ruehle and C. Junghans, Macromol. Theory Simul. 20, 472 (2011) * Relative entropy and optimization-driven coarse-graining methods in VOTCA, S. Y. Mashayak, M. N. Jochum, K. Koschke, N. R. Aluru, V. Ruehle, and C. Junghans, to appear in PLoS ONE (2015) In case of questions, please post them in the google discussion group for votca at http://groups.google.com/group/votca You can contact the VOTCA Development Team at email@example.com. The following tutorials (compare with paper above) are included. They all rely on Gromacs unless specified otherwise: spce/atomistic atomistic reference simulations for SPC/E water spce/force_matching force matching for SPC/E water spce/ibi iterative boltzmann inversion for SPC/E water spce/ibi_pressure iterative boltzmann inversion for SPC/E water with simple pressure correction spce/ibi_pressure_wjk iterative boltzmann inversion for SPC/E water with wjk pressure correction spce/ibi_hoomd-blue iterative boltzmann inversion for SPC/E water using hoomd-blue spce/ibi_dlpoly iterative boltzmann inversion for SPC/E water using dl_poly spce/ibi_espresso iterative boltzmann inversion for SPC/E water using ESPResSo spce/ibi_espressopp iterative boltzmann inversion for SPC/E water using ESPResSo++ spce/ibi_lammps iterative boltzmann inversion for SPC/E water using LAMMPS spce/ibi_gromacs-multi iterative boltzmann inversion for SPC/E water using GROMACS' multidir feature spce/imc inverse monte carlo for SPC/E water spce/re relative entropy method for SPC/E water spce/re_lammps relative entropy method for SPC/E water using LAMMPS spce/realtime iterative boltzmann inversion realtime tutorial for SPC/E water spce/realtime_lammps iterative boltzmann inversion realtime tutorial for SPC/E water using LAMMPS spce/simplex simplex optimization for SPC/E water spce/simplex/simple optimizing the rdf spce/simplex/pressure optimizing the rdf and pressure spce/simplex/density optimizing the rdf and density spce/cma cma optimization for SPC/E water spce/cma/simple optimizing the rdf spce/cma/density optimizing the rdf and the density methanol/atomistic atomistic simulations for methanol methanol/force_matching force matching for methanol methanol/ibi iterative boltzmann inversion for methanol methanol/imc inverse monte carlo for methanol methanol/imc_gromacs-remd inverse monte carlo for methanol with REMD (only for gromacs) during iterations propane/atomistic atomistic simulations for liquid propane propane/ibi iterative boltzmann inversion for nonbonded interactions of liquid propane propane/imc inverse monte carlo for nonbonded interactions of liquid propane propane/single_chain atomistic simulations, boltzmann inversion and force matching for a single chain of propane hexane/atomistic atomistic simulations for liquid hexane hexane/force_matching force matching (bonded and nonbonded interactions of liquid hexane hexane/ibi_all iterative boltzmann inversion for bonded and nonbonded interactions of liquid hexane hexane/ibi_nonbonded iterative boltzmann inversion for only nonbonded interactions of liquid hexane hexane/hybrid_force_matching hybrid force matching of only nonbonded interactions (with bonded interactions from boltzmann inversion) methanol-water methanol-water mixture for 3 different concentrations methanol-water/*/atomistic atomistic simulations methanol-water/*/re relative entropy method methanol-water/*/simplex simplex optimizing urea-water/atomistic atomistic reference simulations urea-water mixture urea-water/kb-ibi Kirkwood-Buff coarse-graining (see Ganguly et al. J. Chem. Theo. Comp., 8, 1802 (2012) for details) urea-water/cibi Coordination iterative Boltzmann inversion (see T. E. de Oliveira et al., JCP 144, 174106 (2016) for details) - different molarity than kb-ibi urea-water/cibi/pre IBI preparation run for cibi urea-water/ibi boltzmann inversion (to compare to kb-ibi) LJ1-LJ2/imc regularization of inverse Monte-Carlo (see Rosenberger et al. Eur. Phys. J. Special Topics 225, 1323-1345 (2016) for details) each of the tutorials contains a run.sh which lists all commands needed to execute the tutorial.