“Comparison of force field implementations”的意思、由来-开放百科全书

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Comparison of force field implementations

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This is a table of computer programs implementing molecular mechanics force fields.

Program	OPLS	AMBER	CHARMM	GAFF	MMFF	QVBMM	UFF	Comments
Abalone	UA}}	94, 96, 99SB, 03, GS, ii, Automatic FF generator^[1]}}	{{no}}	{{no}}	{{no}}	{{no}}	UFF-Dreiding-like field}}	For proteins, DNA, ligands
ACEMD	{{yes}}	{{yes}}	{{yes}}	{{yes}}	{{no}}	{{no}}	{{no}}
AMBER	{{yes}}	{{yes}}	Via chamber tool since v11}}	{{yes}}	{{no}}	{{no}}	{{no}}
ArgusLab	{{no}}	{{yes}}	{{no}}	{{no}}	{{no}}	{{no}}	{{yes}}	Addition to quantum chemistry
Ascalaph Designer	UA}}	94, 99SB, 03}}	{{no}}	{{no}}	{{no}}	{{no}}	{{no}}
Avogadro	{{no}}	{{no}}	{{no}}	{{yes}}	94, 94s}}	{{no}}	{{yes}}
Balloon	{{no}}	{{no}}	{{no}}	{{no}}	94}}	{{no}}	{{no}}	MMFF94-like
BOSS	{{yes}}	{{no}}	{{no}}	{{no}}	{{no}}	{{no}}	{{no}}
CHARMM	{{yes}}*	{{yes}}*	{{yes}}*	Via CHARMM-GUI}}^[2]	Full MMFF94, but code rumored unmaintained}}	{{no}}	{{no}}	* in standard distribution
chemkit	{{yes}}	{{yes}}	{{no}}	{{no}}	{{yes}}	{{no}}	{{yes}}
Gabedit	{{no}}	{{yes}}	{{no}}	{{yes}}	{{yes}}	{{no}}	{{no}}
Gaussian mm utility	{{no}}	{{yes}}	{{no}}	{{no}}	{{no}}	{{no}}	{{yes}}	Dreiding field available
GROMACS	{{yes}}	{{yes}}*	{{yes}}*	{{yes}}	{{no}}	{{no}}	{{no}}	* in standard distribution since v4.5.0
HyperChem	{{yes}}	{{yes}}	As BIO+ implementation}}	{{no}}	{{no}}	{{no}}	{{no}}	MM+ available
MOE	AA}}	89, 94, 99, also with Extended Hückel Theory}}	22, 27}}	{{no}}	94(s)}}	{{no}}	{{no}}
NAMD	{{yes}}	{{yes}}	{{yes}}	{{yes}}	{{no}}	{{no}}	{{no}}
StruMM3D (STR3DI32)	{{no}}	{{no}}	{{no}}	{{no}}	{{no}}	{{yes}}	{{no}}	Molecules and clusters
Q	{{yes}}	{{yes}}	{{yes}}	{{no}}	{{no}}	{{no}}	{{no}}	For biopolymers
Tinker	UA, AA, AA/L}}	94, 96, 98, 99}}	19, 27}}	{{no}}	{{no}}	{{no}}	{{no}}	For proteins, organic molecules
Towhee	UA, AA}}	86}}	19, 22, 27}}	{{no}}	94}}	{{no}}	{{yes}}	Monte Carlo
Yasara	{{no}}	94, 96, 99, 03}}	{{no}}	{{no}}	{{no}}	{{no}}	{{no}}	Plus custom fields for hires refinement

References

1. ^Automatic Force Field generator
2. ^CHARMM-GUI

2 : Force fields|Molecular modelling

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