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|Codacy Badge| |codecov| |CI| |DOI|
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:
- | *Force-matching with three-body interactions in VOTCA*,
| C. Scherer, and D. Andrienko,
| `Phys. Chem. Chem. Phys, 20, 22387–22394
(2018) <http://xlink.rsc.org/?DOI=C8CP00746B>`__.
- | *Relative entropy and optimization-driven coarse-graining methods
in VOTCA*,
| S.Y. Mashayak, M. Jochum, K. Koschke, N.R. Aluru, V. Ruehle, and C.
Junghans,
| `PLoS one 10, e131754
(2015) <http://dx.doi.org/10.1371/journal.pone.0131754>`__.
- | *Hybrid approaches to coarse-graining using the VOTCA package:
liquid hexane*,
| V. Ruehle and C. Junghans,
| `Macromol. Theory Simul. 20, 472
(2011) <http://dx.doi.org/10.1002/mats.201100011>`__.
- | *Versatile Object-oriented Toolkit for Coarse-graining
Applications*,
| V.Ruehle, C. Junghans, A. Lukyanov, K. Kremer, and D. Andrienko,
| `J. Chem. Theo. Comp. 5 (12), 3211
(2009) <http://dx.doi.org/10.1021/ct900369w>`__.
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. A detailed guide can be found in:
`Tutorial <https://www.votca.org/csg-tutorials/Tutorial.html>`__.
- ``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
- ``spce/3body_sw``: force matching for SPC/E water with 3body SW interactions
- ``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.
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