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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 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/ibi boltzmann inversion
each of the tutorials contains a run.sh which lists all commands
needed to execute the tutorial.
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