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 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_PTM_Hassan21.v1 SBM_AA-amber-bonds with modified RNA residues added Asem Hassan N/A 2.4
AA_ions_Wang21.v1 Effective ion potentials with AMBER bonded geometry Ailun Wang N/A 2.4.2 1,2

AA_coulomb_Wang21.v1 SMOG model with AMBER bonded geometry and charges Ailun Wang N/A 2.4.2 1,2

AA_12-18_Wang21.v1 SMOG model 12-18 non-bonded terms and AMBER bonded geometry Ailun Wang N/A 2.4.2 1,2

Notes

N/A: templates will be released upon publication.

1: Gromacs Support: These templates generate files that are only 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

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_PTM_Hassan21.v1	SBM_AA-amber-bonds with modified RNA residues added	Asem Hassan		N/A		2.4
AA_ions_Wang21.v1	Effective ion potentials with AMBER bonded geometry	Ailun Wang		N/A		2.4.2	1,2
AA_coulomb_Wang21.v1	SMOG model with AMBER bonded geometry and charges	Ailun Wang		N/A		2.4.2	1,2
AA_12-18_Wang21.v1	SMOG model 12-18 non-bonded terms and AMBER bonded geometry	Ailun Wang		N/A		2.4.2	1,2