coarse-graining tutorials
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LJ1-LJ2/imc
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README

README

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.