Comparison of force-field implementations: Difference between revisions

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This is a table of computer programs implementing [[molecular mechanics]] [[Force field (chemistry) | '''force fields''']].

This is a table of notable computer programs implementing [[molecular mechanics]] [[Force field (chemistry)|force fields]]. <!-- Only for programs/packages with their own article. Packages without article will be removed. -->

{| class="wikitable"

|-

! [[Computer program|Program]]

!

! [[OPLS ]]

! [[AMBER]]

! [[CHARMM]]

! [[AMBER#Parameter_setsParameter sets|GAFF]]

! [[Merck Molecular Force Field | MMFF]]

! QVBMM

! [[Universal force field|UFF]]

!UFF

! -

! Comments

|-

| [[Abalone (molecular mechanics)|Abalone]]

|[http://www.biomolecular-modeling.com/Abalone/index.html Abalone]

| {{yes|UA}}

| {{yes|94, 96, 99SB, 03, GS, ii, Automatic FF generator<ref>[http://www.biomolecular-modeling.com/FF/index.html Automatic Force Field generator]</ref>}}

|94, 96, 99SB, 03, GS, i

| {{no}}

|

| {{no}}

|

| {{no}}

|

| {{no}}

|

| {{yes|UFF-[[André Dreiding|Dreiding]]-like field}}

|

| For [[protein]]s, [[DNA]], ligands

| ('''+''')<ref>UFF/DREIDING like force field</ref>

|for proteins and DNA

|-

| [[AMBER]]

|ACEMD

| {{yes}}

|'''+'''

| {{yes}}

|'''+'''

| {{yes|Via ''chamber'' tool since v11}}

|'''+'''

| {{yes}}

|'''+'''

| {{no}}

|

| {{no}}

|

| {{no}}

|

|

|

|-

| [[AMBERAscalaph Designer]]

| {{yes|UA}}

|'''+'''

| {{yes|94, 99SB, 03}}

|'''+'''

| {{no}}

|'''+'''<ref>CHARMM force field via "chamber" tool since v11</ref>

| {{no}}

|'''+'''

| {{no}}

|

| {{no}}

|

| {{no}}

|

|

|

|-

| [[Avogadro (software)|Avogadro]]

|[http://www.arguslab.com/ ArgusLab]

| {{no}}

|

| {{no}}

|'''+'''

| {{no}}

|

| {{yes}}

|

| {{yes|94, 94s}}

|

| {{no}}

|

| {{yes}}

|'''+'''

|

| addition to Quantum Chemistry

|-

| [[Ascalaph DesignerBalloon]]

| {{no}}

|UA

| {{no}}

|94, 99SB, 03

| {{no}}

|

| {{no}}

|

| {{yes|94}}

|

| {{no}}

|

| {{no}}

|

| MMFF94-like

|

|

|-

| [[BOSS (molecular mechanics)|BOSS]]

|[[Avogadro (software) | Avogadro]]

| {{yes}}

|

| {{no}}

|

| {{no}}

|

| {{no}}

|'''+'''

| {{no}}

|94, 94s

| {{no}}

|

| {{no}}

|'''+'''

|

|-

| [[CHARMM]]

|[http://users.abo.fi/mivainio/balloon/ Balloon]

| {{yes}}*

|

| {{yes}}*

|

| {{yes}}*

|

| {{yes|Via CHARMM-GUI}}<ref>[http://www.charmm-gui.org/ CHARMM-GUI]</ref>

|

| {{some|Full MMFF94, but code rumored unmaintained}}

|

| {{no}}

|94

| {{no}}

|

| * in standard distribution

|

|"MMFF94-like"

|-

| [[Gabedit]]

|[[BOSS (molecular mechanics)|BOSS]]

| {{no}}

|'''+'''

| {{yes}}

|

| {{no}}

|

| {{yes}}

|

| {{yes}}

|

| {{no}}

|

| {{no}}

|

|

|

|-

| [[Gaussian (software)|Gaussian]] mm utility

|[[CHARMM]]

| {{no}}

|'''+'''

| {{yes}}

|'''+'''

| {{no}}

|'''+'''

| {{no}}

|'''+'''<ref>Through [http://www.charmm-gui.org/ CHARMM-GUI]</ref>

| {{no}}

|'''~'''<ref>Full MMFF94 implementation within CHARMM but code is rumored to have fallen in disrepair</ref>

| {{no}}

|

| {{yes}}

|

| [[André Dreiding|Dreiding]] field available

|

|CHARMM, AMBER and OPLS force fields are included in the standard CHARMM distribution

|-

| [[GROMACS]]

|[http://www.chemkit.org chemkit]

| {{yes}}

|'''+'''

| {{yes}}*

|'''+'''

| {{yes}}*

|

| {{yes}}

|

| {{no}}

|'''+'''

| {{no}}

|

| {{no}}

|'''+'''

| * in standard distribution since v4.5.0

|

|-

| [[Molecular Operating Environment|MOE]]

|[[Gabedit]]

| {{yes|AA}}

|

| {{yes|89, 94, 99, also with Extended Hückel Theory}}

|'''+'''

| {{yes|22, 27}}

|

| {{no}}

|

| {{yes|94(s)}}

|

| {{no}}

|

| {{no}}

|

|

|

|-

| [[NAMD]]

|[[Gaussian (software)|Gaussian mm utility]]

| {{yes}}

|

| {{yes}}

|'''+'''

| {{yes}}

|

| {{yes}}

|

| {{no}}

|

| {{no}}

|

| {{no}}

|

|

|'''+'''

|DREIDING force field is also available

|-

| [[GROMACSOpenbabel]]

| {{no}}

|'''+'''

| {{yes}}

|'''+'''

| {{no}}

|'''+'''

| {{yes}}

|'''+'''

| {{yes|94, 94s}}

| {{no}}

| {{yes}}

|

|

|

|

|CHARMM and AMBER force fields are included in the standard Gromacs distribution since 4.5.0

|-

| [[Q (software)|Q]]

|HyperChem

| {{yes}}

|'''+'''

| {{yes}}

|'''+'''

| {{yes}}

|'''(+)'''<ref>as BIO+ implementation</ref>

| {{no}}

|

| {{no}}

|

| {{no}}

|

| {{no}}

|

| For [[biopolymer]]s

|

|MM+ is also available

|-

| [[Tinker (software)|Tinker]]

|[http://www.chemcomp.com/ MOE]

| {{yes|UA, AA, AA/L}}

|AA

|89, {{yes|94, 96, 98, 99}}

|22 {{yes|19, 27}}

| {{no}}

|

| {{yes|94(s)}}

| {{no}}

|

| {{no}}

|

| For [[protein]]s, [[Organic compound|organic molecules]]

|

|-

| [[NAMDYasara]]

| {{no}}

|'''+'''

| {{yes|94, 96, 99, 03}}

|'''+'''

| {{no}}

|'''+'''

| {{no}}

|'''+'''

| {{no}}

|

| {{no}}

|

| {{no}}

|

| Plus custom fields for hires refinement

|

|

|-

|[http://www.exorga.com/ StruMM3D (STR3DI32)]

|

|

|

|

|

|'''+'''

|

|molecules and clusters

|-

|[[Q (software)|Q]]

|'''+'''

|'''+'''

|'''+'''

|

|

|

|

| for biopolymers

|-

|[[TINKER]]

|UA, AA, AA/L

|94, 96, 98, 99

|19, 27

|

|

|

|

|

| for proteins and organic molecules

|-

|[http://towhee.sourceforge.net/ Towhee]

|UA, AA

|86

|19, 22, 27

|

|94

|

|'''+'''

| Monte Carlo

|-

|[[Yasara]]

|

|94,96,99,03

|

|

|

|

|

|

|Plus custom force fields for hires refinement

|-

|}

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*[[Molecular design software]]

*[[Molecule editor]]

*[[ListComparison of software for molecular mechanics modeling|Software for molecular mechanics modeling]]

*[[Molecular modeling on GPU]]

Line 252 ⟶ 189:

{{Reflist}}

[[Category:Force fields (chemistry)]]

[[Category:Molecular modelling]]

[[Category:Software comparisons]]