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Merge pull request #69 from openforcefield/opc3
OPC3, TIP4P-FB, and ions for TIP3P-FB
2 parents fbf5695 + 8f2bd76 commit 0c5527a

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‎.github/workflows/CI.yml‎

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if: ${{ matrix.toolkit == true }}
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run: |
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python scripts/get_ion_nb_params_from_ambertools_frcmod.py $AMBERHOME/dat/leap/parm/frcmod.ionslm_126_opc
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python scripts/get_ion_nb_params_from_ambertools_frcmod.py $AMBERHOME/dat/leap/parm/frcmod.ionslm_126_opc3
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python scripts/get_ion_nb_params_from_ambertools_frcmod.py $AMBERHOME/dat/leap/parm/frcmod.ionslm_126_fb3
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python scripts/get_ion_nb_params_from_ambertools_frcmod.py $AMBERHOME/dat/leap/parm/frcmod.ionslm_126_fb4
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ls scripts/write_*.py | xargs -n 1 -P 3 python
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- name: Error out if any OFFXML files changed

‎README.md‎

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@@ -26,8 +26,12 @@ Details for each force field in this repository can be found in the following ta
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| Filename | DOI | FF line | Release Date | Major format changes? |
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|---------------------------------------------|-----------------------------------------------------------------------------------------------------------|---------|---------------|-----------------------|
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| `openff-2.1.0.offxml` | [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.7889050.svg)](https://doi.org/10.5281/zenodo.7889050) | Sage | May 2, 2023 | No |
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| `openff_unconstrained-2.1.0.offxml` | [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.7889050.svg)](https://doi.org/10.5281/zenodo.7889050) | Sage | May 2, 2023 | No |
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| `opc-1.0.1.offxml` | see `docs/water-models.md` | Ports | May 24, 2023 | No |
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| `opc3-1.0.0.offxml` | see `docs/water-models.md` | Ports | May 24, 2023 | No |
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| `tip3p_fb-1.1.0.offxml` | see `docs/water-models.md` | Ports | May 24, 2023 | No |
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| `tip4p_fb-1.0.0.offxml` | see `docs/water-models.md` | Ports | May 24, 2023 | No |
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| `openff-2.1.0.offxml` | [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.7889050.svg)](https://doi.org/10.5281/zenodo.7889050) | Sage | May 2, 2023 | No |
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| `openff_unconstrained-2.1.0.offxml` | [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.7889050.svg)](https://doi.org/10.5281/zenodo.7889050) | Sage | May 2, 2023 | No |
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| `opc-1.0.0.offxml` | see `docs/water-models.md` | Ports | May 1, 2023 | No |
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| `openff-2.1.0-rc.1.offxml` | | Sage | Apr 10, 2023 | No |
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| `openff_unconstrained-2.1.0-rc.1.offxml` | | Sage | Apr 10, 2023 | No |
@@ -144,6 +148,8 @@ Force fields moving forward will be called `name-X.Y.Z`
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- `2023.05.1`: This release adds `openff-2.1.0.offxml`, Sage 2.1.0, with identical physics parameters to `openff-2.1.0-rc.1.offxml`.
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- `2023.06.0`: This release adds `opc-1.0.1.offxml`, standardizing the use of the string "kilocalorie_per_mole". It also adds `tip3p-fb-1.1.0.offxml`, which fixes a unit error in the geometric constraints and adds additional ion parameters. Finally, it adds `opc3-1.0.0.offxml` and `tip4p_fb-1.0.0.offxml`.
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#### Acknowledgements
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Project based on the

‎docs/water-models.md‎

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* [TIP3P](https://doi.org/10.1063/1.445869)
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* [TIP3P-FB](https://doi.org/10.1021/jz500737m)
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* [TIP4P-FB](https://doi.org/10.1021/jz500737m)
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* [OPC](https://doi.org/10.1021/jz501780a)
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* [OPC3](https://doi.org/10.1063/1.4960175)
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The TIP3P file includes monovalent ion parameters from [Juong and Cheatham](https://dx.doi.org/10.1021/jp8001614).
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The OPC file includes the 12-6 hydration free energy (HFE) monovalent ion parameters from [Sengupta et al. 2021](https://doi.org/10.1021/acs.jcim.0c01390), the 12-6 compromise (CM) divalent ion parameters from [Li et al. 2020](https://doi.org/10.1021/acs.jctc.0c00194), and the 12-6 ion-oxygen distance (IOD) trivalent and tetravalent ion parameters from [Li et al. 2021](https://doi.org/10.1021/acs.jctc.0c01320).
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The OPC, OPC3, TIP3P-FB, and TIP4P-FB files includes the 12-6 hydration free energy (HFE) monovalent ion parameters from [Sengupta et al. 2021](https://doi.org/10.1021/acs.jcim.0c01390), the 12-6 compromise (CM) divalent ion parameters from [Li et al. 2020](https://doi.org/10.1021/acs.jctc.0c00194), and the 12-6 ion-oxygen distance (IOD) trivalent and tetravalent ion parameters from [Li et al. 2021](https://doi.org/10.1021/acs.jctc.0c01320).
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These files are not original force fields made by Open Force Field.
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Instead they are ports of existing force fields into the [SMIRNOFF](https://openforcefield.github.io/standards/standards/smirnoff/) force field format.

‎openforcefields/data/README.md‎

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* `jc.csv`: Data taken from Table 5 in https://pubs.acs.org/doi/10.1021/jp8001614
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* `ionslm_126_opc.csv` taken from $AMBERHOME/dat/leap/parm/frcmod.ionslm_126_opc in ambertools-22.0-py310h206695f
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* `ionslm_126_opc3.csv` taken from $AMBERHOME/dat/leap/parm/frcmod.ionslm_126_opc3 in ambertools-22.0-py310h206695f
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* `ionslm_126_fb3.csv` taken from $AMBERHOME/dat/leap/parm/frcmod.ionslm_126_fb3 in ambertools-22.0-py310h206695f
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* `ionslm_126_fb4.csv` taken from $AMBERHOME/dat/leap/parm/frcmod.ionslm_126_fb4 in ambertools-22.0-py310h206695f

‎openforcefields/data/ionslm_126_fb3.csv‎

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element,rmin_half (Angstrom),epsilon (kcal/mol)
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Li+,1.26,0.0028218
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Na+,1.459,0.02759452
4+
K+,1.705,0.14158262
5+
Rb+,1.802,0.21475916
6+
Cs+,1.97,0.36217399
7+
Tl+,1.676,0.12244452
8+
Cu+,1.192,0.00096394
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Ag+,1.328,0.00699604
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F-,1.834,0.24140216
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Cl-,2.3,0.63803333
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Br-,2.481,0.75027433
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I-,2.742,0.86005879
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Be2+,0.963,4.89e-06
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Cu2+,1.223,0.0016086
16+
Ni2+,1.257,0.0027012
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Pt2+,1.274,0.0034452
18+
Zn2+,1.276,0.00354287
19+
Co2+,1.304,0.00516628
20+
Pd2+,1.308,0.00544088
21+
Ag2+,1.339,0.00799176
22+
Cr2+,1.349,0.00899152
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Fe2+,1.356,0.00974813
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Mg2+,1.363,0.01055378
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V2+,1.366,0.01091456
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Mn2+,1.411,0.01755812
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Hg2+,1.411,0.01755812
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Cd2+,1.415,0.01827024
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Yb2+,1.629,0.09454081
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Ca2+,1.635,0.09788018
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Sn2+,1.652,0.1076997
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Pb2+,1.73,0.15917293
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Eu2+,1.782,0.19865859
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Sr2+,1.789,0.20424131
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Sm2+,1.795,0.20907204
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Ba2+,1.983,0.37399087
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Ra2+,1.983,0.37399087
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Al3+,1.287,0.00412163
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Fe3+,1.419,0.0190038
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Cr3+,1.364,0.01067299
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In3+,1.445,0.02431873
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Tl3+,1.496,0.03776169
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Y3+,1.6,0.07934493
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La3+,1.731,0.1598965
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Ce3+,1.754,0.17693975
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Pr3+,1.746,0.17092614
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Nd3+,1.692,0.13282966
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Sm3+,1.667,0.11679623
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Eu3+,1.675,0.12180998
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Gd3+,1.625,0.09235154
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Tb3+,1.633,0.09675968
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Dy3+,1.608,0.08337961
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Er3+,1.6,0.07934493
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Tm3+,1.6,0.07934493
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Lu3+,1.583,0.07117158
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Hf4+,1.489,0.03566355
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Zr4+,1.508,0.04155519
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Ce4+,1.705,0.14158262
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U4+,1.705,0.14158262
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Pu4+,1.682,0.12628793
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Th4+,1.718,0.15060822

‎openforcefields/data/ionslm_126_fb4.csv‎

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element,rmin_half (Angstrom),epsilon (kcal/mol)
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Li+,1.24,0.00209587
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Na+,1.448,0.02499549
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K+,1.685,0.1282327
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Rb+,1.795,0.20907204
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Cs+,1.95,0.34401021
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Tl+,1.666,0.11617738
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Cu+,1.172,0.00067804
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Ag+,1.313,0.0058006
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F-,1.845,0.25078
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Cl-,2.313,0.64716164
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Br-,2.454,0.73554824
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I-,2.804,0.87867445
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Be2+,0.924,1.42e-06
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Cu2+,1.181,0.00089969
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Ni2+,1.213,0.00136949
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Pt2+,1.229,0.00176831
18+
Zn2+,1.234,0.00191142
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Co2+,1.277,0.00359255
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Pd2+,1.282,0.00384964
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Ag2+,1.316,0.00602547
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Cr2+,1.327,0.00691068
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Fe2+,1.334,0.00752608
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Mg2+,1.342,0.00828195
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V2+,1.345,0.00858042
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Mn2+,1.394,0.01476261
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Hg2+,1.394,0.01476261
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Cd2+,1.398,0.01538757
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Yb2+,1.621,0.09019198
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Ca2+,1.627,0.09344247
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Sn2+,1.645,0.10359269
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Pb2+,1.728,0.15773029
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Eu2+,1.782,0.19865859
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Sr2+,1.789,0.20424131
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Sm2+,1.796,0.20988115
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Ba2+,1.992,0.38216886
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Ra2+,1.992,0.38216886
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Al3+,1.267,0.00312065
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Fe3+,1.404,0.01636246
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Cr3+,1.345,0.00858042
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In3+,1.443,0.02387506
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Tl3+,1.488,0.03537062
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Y3+,1.583,0.07117158
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La3+,1.715,0.1485017
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Ce3+,1.738,0.16500296
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Pr3+,1.731,0.1598965
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Nd3+,1.675,0.12180998
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Sm3+,1.65,0.10651723
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Eu3+,1.658,0.11129023
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Gd3+,1.608,0.08337961
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Tb3+,1.617,0.08806221
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Dy3+,1.592,0.07543075
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Er3+,1.583,0.07117158
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Tm3+,1.583,0.07117158
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Lu3+,1.567,0.06397679
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Hf4+,1.467,0.02960343
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Zr4+,1.495,0.03745682
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Ce4+,1.692,0.13282966
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U4+,1.692,0.13282966
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Pu4+,1.667,0.11679623
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Th4+,1.709,0.14433113

‎openforcefields/data/ionslm_126_opc.csv‎

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element,opc_rmin2 (A),opc_eps (kcal/mol)
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element,rmin_half (Angstrom),epsilon (kcal/mol)
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Li+,1.242,0.00216058
33
Na+,1.467,0.02960343
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K+,1.702,0.13953816

‎openforcefields/data/ionslm_126_opc3.csv‎

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element,rmin_half (Angstrom),epsilon (kcal/mol)
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Li+,1.27,0.0032565
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Na+,1.469,0.0301216
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K+,1.703,0.14021803
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Rb+,1.8,0.21312875
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Cs+,1.965,0.35762995
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Tl+,1.682,0.12628793
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Cu+,1.201,0.001123
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Ag+,1.335,0.00761745
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F-,1.818,0.2279546
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Cl-,2.306,0.64226672
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Br-,2.501,0.76074098
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I-,2.78,0.87175814
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Be2+,0.971,6.21e-06
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Cu2+,1.228,0.0017408
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Ni2+,1.251,0.00247282
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Pt2+,1.272,0.00334975
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Zn2+,1.28,0.00374505
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Co2+,1.306,0.00530214
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Pd2+,1.309,0.00551135
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Ag2+,1.339,0.00799176
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Cr2+,1.349,0.00899152
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Fe2+,1.356,0.00974813
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Mg2+,1.363,0.01055378
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V2+,1.366,0.01091456
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Mn2+,1.41,0.0173834
27+
Hg2+,1.41,0.0173834
28+
Cd2+,1.413,0.01791152
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Yb2+,1.622,0.09072908
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Ca2+,1.628,0.09399072
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Sn2+,1.641,0.10128575
32+
Pb2+,1.723,0.15415012
33+
Eu2+,1.772,0.19078645
34+
Sr2+,1.778,0.1954949
35+
Sm2+,1.784,0.2002477
36+
Ba2+,1.966,0.35853865
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Ra2+,1.966,0.35853865
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Al3+,1.287,0.00412163
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Fe3+,1.419,0.0190038
40+
Cr3+,1.364,0.01067299
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In3+,1.453,0.02615377
42+
Tl3+,1.496,0.03776169
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Y3+,1.6,0.07934493
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La3+,1.733,0.16134811
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Ce3+,1.758,0.1799796
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Pr3+,1.75,0.17392181
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Nd3+,1.692,0.13282966
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Sm3+,1.667,0.11679623
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Eu3+,1.675,0.12180998
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Gd3+,1.625,0.09235154
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Tb3+,1.633,0.09675968
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Dy3+,1.608,0.08337961
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Er3+,1.6,0.07934493
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Tm3+,1.6,0.07934493
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Lu3+,1.583,0.07117158
56+
Hf4+,1.489,0.03566355
57+
Zr4+,1.508,0.04155519
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Ce4+,1.708,0.1436416
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U4+,1.708,0.1436416
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Pu4+,1.682,0.12628793
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Th4+,1.721,0.15272873

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