[gmx-users] on the force field

David van der Spoel spoel at xray.bmc.uu.se
Wed Mar 28 13:07:12 CEST 2012


On 2012-03-28 13:02, Acoot Brett wrote:
>
> Dear All,
>
> Does anyone can make an introduction on the differences among the
> following force fields for protein? Which are much easy to be accepted
> for publication purpose?

Try reading some literature. Search for protein force field simulation.

>
> Cheers,
>
> Acoot
>
>   1: AMBER03 force field (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003)
>   2: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)
>   3: AMBER96 force field (Kollman et al., Acc. Chem. Res. 29, 461-469, 1996)
>   4: AMBER99 force field (Wang et al., J. Comp. Chem. 21, 1049-1074, 2000)
>   5: AMBER99SB force field (Hornak et al., Proteins 65, 712-725, 2006)
>   6: AMBER99SB-ILDN force field (Lindorff-Larsen et al., Proteins 78, 1950-58, 2010)
>   7: AMBERGS force field (Garcia&
>   Sanbonmatsu, PNAS 99, 2782-2787, 2002)
>   8: CHARMM27 all-atom force field (with CMAP) - version 2.0
>   9: GROMOS96 43a1 force field
> 10: GROMOS96 43a2 force field (improved alkane dihedrals)
> 11: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
> 12: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
> 13: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
> 14: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
> 15: [DEPRECATED] Encad all-atom force field, using full solvent charges
> 16: [DEPRECATED] Encad all-atom force field, using scaled-down vacuum charges
> 17: [DEPRECATED] Gromacs force field (see manual)
> 18: [DEPRECATED] Gromacs force field with hydrogens for NMR
>
>
>
>


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se



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