GROMACS
GROMACS [1] [2] [3] (GROningen MAchine for Chemical Simulations) is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. GROMACS 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 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 Particle-Mesh-Ewald, arbitrary forms of non-bonded interactions, and implicit solvent Generalized Born methods [4]
Constraint algorithms
GROMACS can use either the SHAKE or the LINCS algorithms [5].
Force fields
GRMACS comes with the following force fields [6][7]
- AMBER
- amber03
- amber94
- amber96
- amber99
- amber99sb
- amber99sb-ildn
- amberGS
- CHARMM
- charmm27
- ENCAD
- encads
- encadv
- gmx2
- gmx
- GROMOS
- gromos43a1
- gromos43a2
- gromos45a3
- gromos53a5
- gromos53a6
- MARTINI
- OPLS-all atom
References
- ↑ 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)
- ↑ 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)
- ↑ 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)
- ↑ source: NVIDIA
- ↑ GROMACS 4 Manual § 3.6
- ↑ Source: /usr/share/gromacs/top for gromacs-4.5.5
- ↑ GROMACS 4.5.6 manual § 4.10