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| .. | | 03-May-2022 | - |
| CMakeModules/ | H | 19-Sep-2021 | - | 202 | 178 |
| LJ1-LJ2/imc/ | H | 19-Sep-2021 | - | 7,584 | 7,459 |
| guide/ | H | 19-Sep-2021 | - | 562 | 448 |
| hexane/ | H | 19-Sep-2021 | - | 39,668 | 39,309 |
| methanol/ | H | 19-Sep-2021 | - | 19,275 | 18,993 |
| methanol-water/ | H | 19-Sep-2021 | - | 103,465 | 102,752 |
| propane/ | H | 19-Sep-2021 | - | 32,386 | 32,022 |
| scripts/ | H | 03-May-2022 | - | 20 | 12 |
| spce/ | H | 19-Sep-2021 | - | 94,352 | 93,004 |
| urea-water/ | H | 19-Sep-2021 | - | 140,852 | 140,455 |
| README.rst | H A D | 19-Sep-2021 | 5.9 KiB | 133 | 111 |
README.rst
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