Comparison of force-field implementations: Difference between revisions

Revision as of 13:01, 29 April 2016

Revision as of 18:51, 23 August 2016

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

{| 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

|-

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

| {{yes|UA}}

| {{yes|94, 96, 99SB, 03, GS, i}}

| {{no}}

|

| {{no}}

|

| {{no}}

|

| {{no}}

|

| ('''+''')<ref>{{yes|UFF/DREIDING-[[André Dreiding|Dreiding]]-like force field</ref>}}

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

|for proteins and DNA

|-

| ACEMD

| {{yes}}

|'''+'''

| {{yes}}

|'''+'''

| {{yes}}

|'''+'''

| {{yes}}

|'''+'''

| {{no}}

|

| {{no}}

|

| {{no}}

|

|

|-

| [[AMBER]]

| {{yes}}

|'''+'''

| {{yes}}

|'''+'''

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

| {{yes}}

|'''+'''

| {{no}}

|

| {{no}}

|

| {{no}}

|

|

|-

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

| {{no}}

|

| {{yes}}

|'''+'''

| {{no}}

|

| {{no}}

|

| {{no}}

|

| {{no}}

|

| {{yes}}

|'''+'''

| Addition to [[quantum chemistry]]

| addition to Quantum Chemistry

|-

| [[Ascalaph Designer]]

| {{yes|UA}}

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

| {{no}}

|

| {{no}}

|

| {{no}}

|

| {{no}}

|

| {{no}}

|

|

|-

| [[Avogadro (software) | Avogadro]]

| {{no}}

|

| {{no}}

|

| {{no}}

|

| {{yes}}

|'''+'''

| {{yes|94, 94s}}

| {{no}}

|

| {{yes}}

|'''+'''

|

|-

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

| {{no}}

|

| {{no}}

|

| {{no}}

|

| {{no}}

|

| {{yes|94}}

| {{no}}

|

| {{no}}

|

|" MMFF94-like"

|-

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

| {{yes}}

|'''+'''

| {{no}}

|

| {{no}}

|

| {{no}}

|

| {{no}}

|

| {{no}}

|

| {{no}}

|

|

|-

| [[CHARMM]]

| {{yes}}

|'''+'''

| {{yes}}

|'''+'''

| {{yes}}

|'''+'''

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

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

| {{no}}

|

| {{no}}

|

| Standard distribution has CHARMM, AMBER, OPLS

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

|-

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

| {{yes}}

|'''+'''

| {{yes}}

|'''+'''

| {{no}}

|

| {{no}}

|

| {{yes}}

|'''+'''

| {{no}}

|

| {{yes}}

|'''+'''

|

|-

| [[Gabedit]]

| {{no}}

|

| {{yes}}

|'''+'''

| {{no}}

|

| {{no}}

|

| {{no}}

|

| {{no}}

|

| {{no}}

|

|

|-

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

| {{no}}

|

| {{yes}}

|'''+'''

| {{no}}

|

| {{no}}

|

| {{no}}

|

| {{no}}

|

| {{yes}}

|'''+'''

|DREIDING force[[André Dreiding|Dreiding]] field is also available

|-

| [[GROMACS]]

| {{yes}}

|'''+'''

| {{yes}}

|'''+'''

| {{yes}}

|'''+'''

| {{yes}}

|'''+'''

| {{no}}

|

| {{no}}

|

| {{no}}

|

|CHARMM and AMBER force fields are included in the standard GromacsStandard distribution since 4v4.5.0 has CHARMM, AMBER

|-

| HyperChem

| {{yes}}

|'''+'''

| {{yes}}

|'''+'''

|'''(+)'''<ref>as {{some|As BIO+ implementation</ref>}}

| {{no}}

|

| {{no}}

|

| {{no}}

|

| {{no}}

|

| MM+ is also available

|-

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

| {{yes|AA}}

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

| {{yes|22, 27}}

| {{no}}

|

| {{yes|94(s)}}

| {{no}}

|

| {{no}}

|

|

|-

| [[NAMD]]

| {{yes}}

|'''+'''

| {{yes}}

|'''+'''

| {{yes}}

|'''+'''

| {{yes}}

|'''+'''

| {{no}}

|

| {{no}}

|

| {{no}}

|

|

|-

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

| {{no}}

|

| {{no}}

|

| {{no}}

|

| {{no}}

|

| {{no}}

|

| {{yes}}

|'''+'''

| {{no}}

|

|molecules [[Molecule]]s and clusters

|-

| [[Q (software)|Q]]

| {{yes}}

|'''+'''

| {{yes}}

|'''+'''

| {{yes}}

|'''+'''

| {{no}}

|

| {{no}}

|

| {{no}}

|

| {{no}}

|

| For [[biopolymer]]s

| for biopolymers

|-

| [[Tinker (software)|Tinker]]

|[[TINKER]]

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

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

| {{yes|19, 27}}

| {{no}}

|

| {{no}}

|

| {{no}}

|

| {{no}}

|

| forFor proteins and[[protein]]s, [[organic moleculesmolecule]]s

|-

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

| {{yes|UA, AA}}

| {{yes|86}}

| {{yes|19, 22, 27}}

| {{no}}

|

| {{yes|94}}

| {{no}}

|

| {{yes}}

|'''+'''

| [[Monte Carlo method|Monte Carlo]]

|-

| [[Yasara]]

| {{no}}

|

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

| {{no}}

|

| {{no}}

|

| {{no}}

|

| {{no}}

|

| {{no}}

|

| Plus custom force fields for hires refinement

|-

|}

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*[[Molecular design software]]

*[[Molecule editor]]

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

*[[Molecular modeling on GPU]]