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| ==Constraint algorithms== | | ==Constraint algorithms== |
| GROMACS can use either the [[SHAKE]] or the [[LINCS]] algorithms <ref>[http://www.gromacs.org/@api/deki/files/82/=gromacs4_manual.pdf GROMACS 4 Manual] § 3.6 </ref>. | | GROMACS can use either the [[SHAKE]] or the [[LINCS]] algorithms <ref>[http://www.gromacs.org/@api/deki/files/82/=gromacs4_manual.pdf GROMACS 4 Manual] § 3.6 </ref>. |
| ==Force fields==
| |
| GROMACS comes with the following [[force fields]] <ref>Source: /usr/share/gromacs/top for gromacs-4.5.5 </ref><ref>GROMACS 4.5.6 manual § 4.10 </ref>
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| * [[AMBER forcefield | AMBER]]
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| ** amber03
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| ** amber94 <ref>[http://dx.doi.org/10.1021/ja00124a002 Wendy D. Cornell , Piotr Cieplak , Christopher I. Bayly , Ian R. Gould , Kenneth M. Merz , David M. Ferguson , David C. Spellmeyer , Thomas Fox , James W. Caldwell , Peter A. Kollman "A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules", Journal of the American Chemical Society (JACS) '''117''' pp. 5179-5197 (1995)]</ref>
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| ** amber96
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| ** amber99
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| ** amber99sb
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| ** amber99sb-ildn
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| ** amberGS <ref>[http://dx.doi.org/10.1073/pnas.042496899 Angel E. García and Kevin Y. Sanbonmatsu "α-Helical stabilization by side chain shielding of backbone hydrogen bonds", PNAS '''99''' pp. 2782-2787 (2002)]</ref>
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|
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| *[[CHARMM]]
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| ** charmm27
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| *[[ENCAD (force field) | ENCAD]]
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| ** encads (full solvent charges)
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| ** encadv (scaled-down vacuum charges)
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| *[[GROMOS]]
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| ** gromos43a1
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| ** gromos43a2
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| ** gromos45a3
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| ** gromos53a5
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| ** gromos53a6
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| *[[MARTINI]]
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| *[[OPLS force field | OPLS-all atom]]
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|
| |
| ==References== | | ==References== |
| <references/> | | <references/> |