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Force fields
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Table of contentsNo headersThese force fields are provided by volunteer contributors on an as-is basis. The GROMACS team implies no warranty by hosting them here. If you plan to use any of these force fields, you should make sure you test them for correctness on your system. Please let people know what you observe (good or bad!).
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|  | 43A1-S3.tar.gz The 43A1-S3 forcefield is an improved forcefield suited for molecular dynamics simulations of lipid bilayers systems. The forcefield has been parameterized in a progressive way, based on the reproduction of molecular volumes and heats of vaporization of small chemical species modelled for the fragments of lipids. This parameter set is validated by MD simulations that replicate experimental structures of bilayers including X-ray form factors, order parameters (J. Phys. Chem. B, 2009, 113, 2748–2763). | 145.42 kB | 22:49, 4 Jan 2011 | schiu | | |  | 53a5.tar.gz The GROMOS 53a5 force field (see J. Comput. Chem. 2004 vol 25 pag 1656) in gromacs format. These files were used to calculate the solvation free-energy for amino-acid side chains and in protein simulations. Please check them before using them in particular if you simulate not-protein systems. Uploaded 13:18 August 30, 2004 by Alessandra Villa (villa at theochem.uni-frankfurt.de) | 58.45 kB | 10:13, 23 May 2009 | rossen | | |  | 53a6.tar.gz The GROMOS 53a6 force field (see J. Comput. Chem. 2004 vol 25 pag 1656) in gromacs format. These files were used to calculate the solvation free-energy for amino-acid side chains and in protein simulations. Please check them before using them in particular if you simulate not-protein systems. Uploaded 13:19 August 30, 2004 by Alessandra Villa (villa at theochem.uni-frankfurt.de) | 58.44 kB | 10:10, 23 May 2009 | rossen | | |  | 56a_CARBO4GROMACS.rar The GROMOS 56a_Carbo [J Comput Chem. 2011; 32 (6): 998-1032] force field in GROMACS format. The files correspond to four types of building blocks based on the beta-D-glucose molecule. | 54.17 kB | 11:42, 7 May 2013 | wojtekp? | | |  | amber12sb.ff.tar.gz ff99SB + new backbone and side chain torsion for protein; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA (see ambertools13) | 310 kB | 14:32, 23 Dec 2015 | mhviet? | | |  | amber14sb.ff.tar.gz For protein: improving the accuracy of the backbone and side chain parameters from ff99SB; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA (more detail, please see amber manual 15) | 300 kB | 14:32, 23 Dec 2015 | mhviet? | |   |  | amber14sb_OL15.ff_corrected-Na-cation-params.tar.gz Amber OL15 force field for DNA and OL3 (chiOL3) force field for RNA, combined with ff14SB protein force field. More details on ffol.upol.cz. Note that in the previous version (present on this web site before 30 August 2019, file name amber14sb_OL15.ff.tar.gz) there was an error in Na+ Joung-Cheatham parameters (epsilon incorrectly 3.65846e-02 instead of the correct value 3.65846e-01 in ffnonbonded.itp file), which is now corrected. Contributed by Petr Jurecka. | 39.11 kB | 08:29, 30 Aug 2019 | mabraham | | |  | amber14sb_parmbsc1.ff.tar.gz ff14SB for protein + parmbsc1 for DNA | 300 kB | 05:27, 5 Dec 2017 | mhviet? | |   |  | amber99bsc1.ff.tgz Amber99 force field Parmbsc1 for DNA (Ivani et al. Nature methods, 13(1), pp.55-58.) This force field has been verified against Amber and gives relative differences on each bonded energy term of 1-2 x 10^-6. Please cite: https://doi.org/10.1371/journal.pcbi.1005463. | 32.31 kB | 14:02, 5 Mar 2018 | viveca | |   |  | amber99sb-ildnp.tgz In addition to AMBER99SB-ILDN, this force field includes improved Pro and Hyp parameters, which were derived from fittings of experimental correlation times and NMR J-couplings. The motional frequency of the Pro ring interconverson predicted by standard AMBER99SB is ~6 times faster than the experimental value, while the current force field reproduces experiment accurately. See Proteins 2014 82 195 for further details. | 37.59 kB | 01:09, 23 Jul 2015 | abil4616? | |   |  | amber99sb-star-ildnp.tgz In addition to AMBER99SB*-ILDN, this force field includes improved Pro and Hyp parameters, which were derived from fittings of experimental correlation times and NMR J-couplings. The motional frequency of the Pro ring interconverson predicted by standard AMBER99SB is ~6 times faster than the experimental value, while the current force field reproduces experiment accurately. See Proteins 2014 82 195 for further details. | 32.43 kB | 01:09, 23 Jul 2015 | abil4616? | | |  | amber99sb_parmbsc0.ff.tgz Amber99sb force field with the ParmBSC0 nucleic acid parameters added (GROMACS 4.5.x format). If you use these files please cite: http://dx.doi.org/10.1016/j.bpj.2012.08.012 in addition to the original force field publications. | 30.79 kB | 10:05, 5 Sep 2012 | TomPiggot | |   |  | CGenffRevB.tar.gz Added sample solvent *.itp files that can be used with sample.top | 449.42 kB | 15:09, 1 Nov 2011 | fabian.casteblanco? | | |  | charmm22star.ff.tgz CHARMM22* force field. Backbone CMAP correction replaced with new torsions (excluding G, P), new partial charges for R, D, and E side chains, and new side chain torsions for D. Adapted from CHARMM27 parameters included with Gromacs 4.5.3. From Piana, S., et al. Biophys J. 2001. 100. L47-L49. | 590 kB | 14:11, 9 Jul 2012 | ktd3? | |   |  | charmm36.ff_4.5.7_ref.tgz GROMACS 4.5.7 version of the CHARMM36 lipid force field with the CHARMM22+CMAP protein force field. These updated CHARMM lipids allow the all-atom simulations of membrane and membrane-protein systems without the use of surface tension. Check out the forcefield.doc for more information regarding these files | 72.69 kB | 14:33, 30 Nov 2015 | TomPiggot | | |  | chcl3_box.tgz.tgz atom types are named opls_X, where X is the OPLS number. Uploaded 10:26 February 12, 2004 by Anonymous (Not e-mail) | 43.25 kB | 10:09, 23 May 2009 | rossen | | |  | ff03-star.tgz ff03* force field, JPCB v113, p9004, 2009. Modification of amber ff03 to match helix-coil data. | 31.63 kB | 11:55, 8 Feb 2011 | rbb24 | | |  | ff03w.tgz ff03w force field (Amber03 adapted for use with Tip4p/2005 water model) | 73.17 kB | 10:28, 18 Aug 2012 | rbb24 | | |  | ff03ws.tgz Amber ff03ws force field with scaled protein-water interactions (JCTC 10:5113, 2014) | 85 kB | 16:16, 11 Sep 2015 | rbb24 | | |  | FF12SB_FF14SB_GROMACS_TEST.tar.bz2 test data set of the force fields, ff99SB, ff12SB and ff15SB , implemented into gromacs | 57.3 MB | 10:02, 24 Dec 2015 | mhviet? | | |  | ff99sb-star-ildn-q.tgz Amber ff99sb with backbone (*), side-chain dihedral (ILDN) and backbone charge (q) modifications (Biophys J,102:1462-1467, 2012) | 32.04 kB | 16:16, 11 Sep 2015 | rbb24 | | |  | ff99sb-star-ildn.tgz Combination of DE-shaw ILDN modifications with ff99SB* force field [JPCB v113, p9004, 2009. Modification of amber ff99SB to match helix-coil data]. | 34.06 kB | 11:55, 8 Feb 2011 | rbb24 | | |  | ff99sb-star.tgz ff99SB* force field, JPCB v113, p9004, 2009. Modification of amber ff99SB to match helix-coil data. | 30.41 kB | 11:55, 8 Feb 2011 | rbb24 | | |  | ff99sbws.tgz Amber ff99SBws force field with scaled protein-water interactions (JCTC 10:5113, 2014) | 96.23 kB | 16:16, 11 Sep 2015 | rbb24 | | |  | ffA2G_test.pdf amber force fields, ff99, ff99SB, ff12SB and ff14SB tested for gromacs implementation | 99.31 kB | 20:25, 27 Dec 2015 | mhviet? | | |  | ffamber_v1.0-doc.tar.gz Several AMBER protein and nucleic acid force fields are available with complete documentation. Please see the ffamber website at http://folding.stanford.edu/ffamber/ for details, as our ports and accompanying documentation will be updated there until integration into future GROMACS distributions. Uploaded 16:55 June 30, 2005 by Eric J. Sorin (esorin at stanford.edu) | 6.04 MB | 10:13, 23 May 2009 | rossen | | |  | ffG43a1p.tar.gz G43a1 modified to contain SEP (phosphoserine), TPO (phosphothreonine), and PTR (phosphotyrosine) (all PO4^{2-} forms), and SEPH, TPOH, PTRH (PO4H^{-} forms). The charges and vdw parameters come from Hansson, Nordlund and Aqvist jmb 265 118-27 1997. They worked mostly with gromos 87 but I generally use gromos 96 so I\'ve made the files in that format (there seem to be no differences in the amino acid charges between 87 and 96). Hansson et al don\'t report bond angle or dihedral parameters, and I don\'t know how to do QM calculations, so I\'ve used the standard forms from the *bon.itp file. For the dihedrals, I\'ve used the 3-fold gd_11. Because of their symmetry, the PO4^{2-} forms at least cannot have the 2-fold + 3-fold symmetry used in the gmx DNA bases. The OP-X LJ-14 parameters are the same as for OA. I\'ve checked that I can build simple 1-molecule topologies and tprs for the PO4H forms, and for the PO4 forms have done 100 ps solvated MD of the isolated am acs and the am acs in proteins (1f1w, 1fu0, 1qmz). I\'ve checked water-phosphate rdfs and parameters in gmxdumped tprs. Uploaded 16:08 May 15, 2002 by Graham Smith (smithgr@cancer.org.uk) | 46.86 kB | 10:13, 23 May 2009 | rossen | | |  | ffG43a2x.tgz The normal version of the GROMOS96 force field results in bad area/lipid and volume/lipid for most lipid membranes. This version of the force field has been extended with new LCH2 and LCH2 united atom types which reproduce the experimental properties of both long hydrocarbons and membranes. Uploaded 17:58 June 08, 2001 by Erik Lindahl (erik@theophys.kth.se) | 44.23 kB | 10:10, 23 May 2009 | rossen | | |  | ffG45a3.tar.gz This force field was created using GROMOS96 43a1 as base and the parameters given by the article An improved GROMOS96 force field for aliphatic hydrocarbons in the condensed phase. Journal of Computational Chemistry 22 (11), August 2001,1205-1218 by Lukas D. Schuler, Xavier Daura, Wilfred F. van Gunsteren. The initial work was performed by christoph riplinger and was later corrected and completed by myself and alessandra villa (villa at theochem.uni-frankfurt.de) who kindly provided the original gromos format file of this force field. Uploaded 17:17 July 19, 2004 by Jaime arce (arce at ibsm.cnrs-mrs.fr) | 46.38 kB | 10:10, 23 May 2009 | rossen | | |  | ffgmx_lipids.tar.gz These are the params from lipid.itp incorporated into the ffgmx*.itp files, as the newer gromacs versions require it. Copy these modified files into the .../gmx/share/top directory or in your current working dir. Uploaded 10:02 January 14, 2003 by Bert de Groot (bgroot@gwdg.de) | 19.91 kB | 10:09, 23 May 2009 | rossen | | |  | ffoplsaanr.tar.gz We added DNA/RNA records to OPLS forcefield. Here you can download version with RESP charges (from Amber). We tested this one more or less. Results you can found at: http://rnp-group.genebee.msu.su/3d/oplsa_ff.html. At that page you can find forcefield with another charges, but this one is not tested. Recently we added 3` and 5` end residues. Scripts that fix pdb to make them compatible with pdb2gmx are here: fixpdb_dna and fixpdb_rna This scripts also works with NA-protein complexes. Uploaded 19:09 March 08, 2005 by Andrey Golovin and Nikita Polyakov (golovin at genebee.msu.su) | 61.27 kB | 10:09, 23 May 2009 | rossen | | |  | gromos43a1p-4.5.1.tgz Force field files for Gromos96 43a1p, re-formatted to be compatible with newer versions of Gromacs (4.0 and beyond). This particular archive organizes the files such that they are compatible with version 4.5.x. Please note that the parameters are unmodified relative to what was contributed by Graham Smith. I take no credit for these parameters; I just made the files compatible with the current version of Gromacs. This version includes files that were missing in the previous tarball. | 64.39 kB | 00:04, 18 Nov 2014 | JLemkul? | | |  | gromos56a6_withAZE_support.zip This is a modified GROMOS 53a6 forcefield that supports non-natural Aze (azetidine-2-carboxylic acid) amino acid that is similar to Proline, except that it has a 4-atom instead of a 5-atom ring. Aze occurs naturally in plants and was shown to have toxic effects in mammalian cells possibly due to its hability to be misincorporated into growing polypeptide chains instead of Proline. We found that Aze has greater propensity to adopt a cis-peptide bond conformation compared to Proline . To install this modified Gromos56a6 forcefield simply unzip the archive in the forcefield folder. Reference: Bessonov K, Vassall KA, Harauz G. Parameterization of the proline analogue Aze (azetidine-2-carboxylic acid) for molecular dynamics simulations and evaluation of its effect on homo-pentapeptide conformations. J Mol Graph Model. 2013 Feb; 39:118-25 | 89.16 kB | 20:40, 24 Feb 2013 | kbessonov? | | |  | GROMOS_56a6_CARBO_R.zip GROMOS 56A6_CARBO_R force field for carbohydrates [Plazinski et al. J. Comp. Chem. 2016, DOI: 10.1002/jcc.24229]. The zip file contains GROMACS .rtp entries and python script allowing to construct the topology for arbitrary linear glucose chains (any linkage/anomery). Sample topologies are included as well. | 84.4 kB | 09:01, 4 Jan 2016 | wojtekp? | | |  | lipid_forcefield.ff.tar.gz All-atomisic force field for phosphatidylcholine lipids. Contains parameters for fully saturated chains, soon unsaturated chains and other head groups will be included. Compatible with the AMBER force fields for proteins. This set of parameters reproduces a lot of experimental data such as area per lipid and thickness(es) but most importantly scattering form factors con order parameters are reproduced. Ref: J. Phys. Chem. B, DOI: 10.1021/jp212503e | 31.36 kB | 16:28, 4 Mar 2012 | joakim? | |
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