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 devs@votca.org.


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/ibi                      boltzmann inversion for SPC/E water
spce/ibi_pressure             boltzmann inversion for SPC/E water with pressure correction
spce/ibi_hoomd-blue           boltzmann inversion for SPC/E water using hoomd-blue
spce/ibi_dlpoly               boltzmann inversion for SPC/E water using dl_poly
spce/ibi_espresso             boltzmann inversion for SPC/E water using ESPResSo
spce/ibi_espressopp           boltzmann inversion for SPC/E water using ESPResSo++
spce/ibi_lammps               boltzmann inversion for SPC/E water using LAMMPS
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                 boltzmann inversion realtime tutorial for SPC/E water
spce/tf                       thermodynamic force example for SPC/E water
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/ibi                  boltzmann inversion for methanol
methanol/ibi_espresso         boltzmann inversion for methanol using ESPResSo
methanol/imc                  inverse monte carlo for methanol

propane/atomistic             atomistic simulations for liquid propane
propane/ibi                   iterative inverse boltzmann 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/ibi                    iterative inverse boltzmann for nonbonded
                              interactions of liquid hexane
hexane/ibi_bonded             iterative inverse boltzmann for bonded & 
                              nonbonded interactions of liquid hexane
hexane/hybrid_force_matching  hybrid force matching (with bonded interaction
                              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)

He-Ar/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. 
