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/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.