Editing GROMACS

[http://www.gromacs.org/ GROMACS] is a versatile package to perform [[molecular dynamics]], i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.

It is primarily designed for biochemical molecules like [[proteins]] and [[lipids]] that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. [[polymers]].

Further information can be found in the wiki dedicated to GROMACS: [http://wiki.gromacs.org/ wiki.gromacs.org].
==References==
#[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)]
#[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)]
[[Category: Materials modeling and Computer simulation codes]]
@@ Line 1: / Line 1: @@
-'''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>
+[http://www.gromacs.org/ GROMACS] is a versatile package to perform [[molecular dynamics]], i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.
-<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] &sect; 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 &sect; 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]]
+It is primarily designed for biochemical molecules like [[proteins]] and [[lipids]] that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. [[polymers]].
+Further information can be found in the wiki dedicated to GROMACS: [http://wiki.gromacs.org/ wiki.gromacs.org].
 ==References==
-<references/>
+#[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)]
-==External links==
+#[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)]
-*[http://www.gromacs.org/ GROMACS home page]
+[[Category: Materials modeling and Computer simulation codes]]
-[[Category: Materials modelling and computer simulation codes]]