GROMACS

2021-10-14T13:30:02Z

145.118.87.250: /* Force fields */

'''GROMACS''' <ref>[http://dx.doi.org/10.1016/0010-4655(95)00042-E H. J. C. Berendsen, D. van der Spoel and R. van Drunen "GROMACS: A message-passing parallel molecular dynamics implementation", Computer Physics Communications '''91''' pp. 43-56 (1995)]</ref>
<ref>[http://dx.doi.org/10.1002/jcc.20291 David Van Der Spoel, Erik Lindahl, Berk Hess, Gerrit Groenhof, Alan E. Mark, Herman J. C. Berendsen "GROMACS: Fast, flexible, and free", Journal of Computational Chemistry '''26''' pp. 1701-1718 (2005)]</ref>
<ref>[http://dx.doi.org/10.1021/ct700301q Berk Hess, Carsten Kutzner, David van der Spoel and Erik Lindahl "GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation", Journal of Chemical Theory and Computation '''4''' pp. 435–447 (2008)]</ref>
('''GRO'''ningen '''MA'''chine for '''C'''hemical '''S'''imulations) is a versatile package to perform [[molecular dynamics]], i.e. simulate the
[[Newtons laws |Newtonian equations of motion]] for systems with hundreds to millions of particles.
GROMACS is primarily designed for [[Biological systems |biochemical molecules]] like [[proteins]] and [[lipids]] that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the non-bonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. [[polymers]].
==GROMACS on Tesla GPUs==
The CUDA port of GROMACS enabling GPU acceleration is now available in beta and supports [[Ewald sum#Particle mesh|Particle-Mesh-Ewald]], arbitrary forms of non-bonded interactions, and implicit solvent Generalized Born methods <ref> source: [http://www.nvidia.com/object/gromacs_on_tesla.html NVIDIA]</ref>
==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>.
==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>
* [[AMBER forcefield | AMBER]]
** amber03
** 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>
** amber96
** amber99
** amber99sb
** amber99sb-ildn
** 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>

*[[CHARMM]]
** charmm27
*[[ENCAD (force field) | ENCAD]]
** encads (full solvent charges)
** encadv (scaled-down vacuum charges)
*[[GROMOS]]
** gromos43a1
** gromos43a2
** gromos45a3
** gromos53a5
** gromos53a6
*[[MARTINI]]
*[[OPLS force field | OPLS-all atom]]

==References==
<references/>
==External links==
*[http://www.gromacs.org/ GROMACS home page]
[[Category: Materials modelling and computer simulation codes]]

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