SMOG 2

SMOG 2 Template Repository

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One of the key features of SMOG 2 is that the force fields are portable. That is, you can share new models by simply making your template files available. Officially-supported force fields (i.e. those tested by smog-check) are included as part of the default distribution. Other force fields are available here. As force fields are integrated within smog-check, they may be moved to the standard SMOG 2 bundle. Most templates will include a README that provides a detailed description of the model. Please note that not all force fields are supported by official versions of Gromacs. If the force field is only intended for use with OpenMM (OpenSMOG) or a modified (i.e. unofficial) version of Gromacs, then it will be indicated in the README. If you would like to have your force field made available, please contact us.

Force Field Name Description Contributor Reference File md5sum SMOG version Notes
SBM_AA+hydrogen AA model with explicit hydrogens Heiko Lammert .gz 1eb45412bf0a2fcc7e6c88539ed9a962
SBM_AA_charged AA model with charges Jeff Noel .gz 9ac52a720689c2b4bd26fb59f257430c
ENM AA model with elastic network for contacts Jeff Noel .gz a9e23114d88e9a6c40672183b126de65
SBM_AA-amber-bonds AA model with bond angles and lengths from AMBER Paul Whitford Viruses, 12, 1273, 2020 .gz 58201035c73acfe3b82b0f202ff4cf14 2.3
AA_glycans_Dodero21.v1 SBM_AA-amber-bonds with glycans added Esteban Dodero Rojas eLife, 10, e70362, 2021 .gz 3d33339bc018d1e098f715c04fc66745 2.4
AA_ions_Wang22.v1 Effective ion potentials with AMBER bonded geometry (Shadow contacts) Ailun Wang JACS, 2022 .gz 391b3be3a90054992940b2e80150c3ca 2.4.4 1,2
AA_ions_cutoff_Wang22.v1 Effective ion potentials with AMBER bonded geometry (cutoff contacts) Ailun Wang JACS, 2022 .gz ea3e6489578879cfa08d0d3f66cb66b6 2.4.4 1,2
AA_12-18_Wang22.v1 SMOG model 12-18 non-bonded terms and AMBER bonded geometry (Shadow contacts) Ailun Wang JACS, 2022 .gz 82a774ebf29c3e579cb0aabff5468bdd 2.4.4 1,2
AA_12-18_cutoff_Wang22.v1 SMOG model 12-18 non-bonded terms and AMBER bonded geometry (cutoff contacts) Ailun Wang JACS, 2022 .gz fab83f2c3a74ce177496cb6726fe5523 2.4.4 1,2
AA_PTM_Hassan21.v1 SBM_AA-amber-bonds with modified RNA residues added Asem Hassan N/A 2.4

Notes

N/A: templates will be released upon publication.

1: Gromacs Support: These templates generate files that are for use with an unofficial modified version of Gromacs 5.1.4 that can be found here.

2: OpenSMOG Support: These templates can be used to generate force fields for use with OpenSMOG v1.1.0, or later.

Page created and maintained by Jeff Noel and Paul Whitford