1|Codacy Badge| |codecov| |CI| |DOI| 2 3This is a collection of coarse-graining tutorials using the VOTCA 4package. Further information on VOTCA can be found at 5http://www.votca.org 6 7The development of VOTCA is mainly funded by academic research grants. 8If you use this package, please cite the VOTCA papers: 9 10- | *Relative entropy and optimization-driven coarse-graining methods 11 in VOTCA*, 12 | S.Y. Mashayak, M. Jochum, K. Koschke, N.R. Aluru, V. Ruehle, and C. 13 Junghans, 14 | `PLoS one 10, e131754 15 (2015) <http://dx.doi.org/10.1371/journal.pone.0131754>`__. 16 17- | *Hybrid approaches to coarse-graining using the VOTCA package: 18 liquid hexane*, 19 | V. Ruehle and C. Junghans, 20 | `Macromol. Theory Simul. 20, 472 21 (2011) <http://dx.doi.org/10.1002/mats.201100011>`__. 22 23- | *Versatile Object-oriented Toolkit for Coarse-graining 24 Applications*, 25 | V.Ruehle, C. Junghans, A. Lukyanov, K. Kremer, and D. Andrienko, 26 | `J. Chem. Theo. Comp. 5 (12), 3211 27 (2009) <http://dx.doi.org/10.1021/ct900369w>`__. 28 29In case of questions, please post them in the google discussion group 30for votca at http://groups.google.com/group/votca 31 32You can contact the VOTCA Development Team at devs@votca.org. 33 34The following tutorials (compare with paper above) are included. They 35all rely on Gromacs unless specified otherwise: 36 37- ``spce/atomistic``: atomistic reference simulations for SPC/E water 38- ``spce/force_matching``: force matching for SPC/E water 39- ``spce/ibi``: iterative boltzmann inversion for SPC/E water 40- ``spce/ibi_pressure``: iterative boltzmann inversion for SPC/E water 41 with simple pressure correction 42- ``spce/ibi_pressure_wjk``: iterative boltzmann inversion for SPC/E 43 water with wjk pressure correction 44- ``spce/ibi_hoomd-blue``: iterative boltzmann inversion for SPC/E 45 water using hoomd-blue 46- ``spce/ibi_dlpoly``: iterative boltzmann inversion for SPC/E water 47 using dl\_poly 48- ``spce/ibi_espresso``: iterative boltzmann inversion for SPC/E water 49 using ESPResSo 50- ``spce/ibi_espressopp``: iterative boltzmann inversion for SPC/E 51 water using ESPResSo++ 52- ``spce/ibi_lammps``: iterative boltzmann inversion for SPC/E water 53 using LAMMPS 54- ``spce/ibi_gromacs-multi``: iterative boltzmann inversion for SPC/E 55 water using GROMACS' multidir feature 56- ``spce/imc`` inverse monte carlo for SPC/E water 57- ``spce/re``: relative entropy method for SPC/E water 58- ``spce/re_lammps``: relative entropy method for SPC/E water using 59 LAMMPS 60- ``spce/realtime``: iterative boltzmann inversion realtime tutorial 61 for SPC/E water 62- ``spce/realtime_lammps``: iterative boltzmann inversion realtime 63 tutorial for SPC/E water using LAMMPS 64- ``spce/simplex``: simplex optimization for SPC/E water 65 66 - ``spce/simplex/simple``: optimizing the rdf 67 - ``spce/simplex/pressure``: optimizing the rdf and pressure 68 - ``spce/simplex/density``: optimizing the rdf and density 69 70- ``spce/cma``: cma optimization for SPC/E water 71 72 - ``spce/cma/simple``: optimizing the rdf 73 - ``spce/cma/density``: optimizing the rdf and the density 74 75- ``methanol/atomistic``: atomistic simulations for methanol 76- ``methanol/force_matching``: force matching for methanol 77- ``methanol/ibi``: iterative boltzmann inversion for methanol 78- ``methanol/imc``: inverse monte carlo for methanol 79- ``methanol/imc_gromacs-remd``: inverse monte carlo for methanol with 80 REMD (only for gromacs) during iterations 81 82- ``propane/atomistic``: atomistic simulations for liquid propane 83- ``propane/ibi``: iterative boltzmann inversion for nonbonded 84 interactions of liquid propane 85- ``propane/imc``: inverse monte carlo for nonbonded interactions of 86 liquid propane 87- ``propane/single_chain``: atomistic simulations, boltzmann inversion 88 and force matching for a single chain of propane 89 90- ``hexane/atomistic``: atomistic simulations for liquid hexane 91- ``hexane/force_matching``: force matching (bonded and nonbonded 92 interactions of liquid hexane 93- ``hexane/ibi_all``: iterative boltzmann inversion for bonded and 94 nonbonded interactions of liquid hexane 95- ``hexane/ibi_nonbonded``: iterative boltzmann inversion for only 96 nonbonded interactions of liquid hexane 97- ``hexane/hybrid_force_matching``: hybrid force matching of only 98 nonbonded interactions (with bonded interactions from boltzmann 99 inversion) 100 101- ``methanol-water``: methanol-water mixture for 3 different 102 concentrations 103 104 - \`methanol-water/\*/atomistic atomistic simulations 105 - ``methanol-water/*/re``: relative entropy method 106 - ``methanol-water/*/simplex``: simplex optimizing 107 108- ``urea-water/atomistic``: atomistic reference simulations urea-water 109 mixture 110- ``urea-water/kb-ibi``: Kirkwood-Buff coarse-graining (see Ganguly et 111 al. J. Chem. Theo. Comp., 8, 1802 (2012) for details) 112- ``urea-water/cibi``: Coordination iterative Boltzmann inversion (see 113 T. E. de Oliveira et al., JCP 144, 174106 (2016) for details) - 114 different molarity than kb-ibi 115- ``urea-water/cibi/pre``: IBI preparation run for cibi 116- ``urea-water/ibi``: boltzmann inversion (to compare to kb-ibi) 117 118- ``LJ1-LJ2/imc``: regularization of inverse Monte-Carlo (see 119 Rosenberger et al. Eur. Phys. J. Special Topics 225, 1323-1345 (2016) 120 for details) 121 122Each of the tutorials contains a ``run.sh`` which lists all commands 123needed to execute the tutorial. 124 125.. |Codacy Badge| image:: https://app.codacy.com/project/badge/Grade/677ff88de55e46ee9411e2eaa6248e0c 126 :target: https://www.codacy.com/gh/votca/csg-tutorials?utm_source=github.com&utm_medium=referral&utm_content=votca/csg-tutorials&utm_campaign=Badge_Grade 127.. |codecov| image:: https://codecov.io/gh/votca/csg-tutorials/branch/master/graph/badge.svg 128 :target: https://codecov.io/gh/votca/csg-tutorials 129.. |CI| image:: https://github.com/votca/votca/workflows/CI/badge.svg?branch=master 130 :target: https://github.com/votca/votca/actions?query=workflow%3ACI+branch%3Amaster 131.. |DOI| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.3902713.svg 132 :target: https://doi.org/10.5281/zenodo.3902713 133