Gromacs

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, lipids and nucleic acids 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


References in zbMATH (referenced in 56 articles )

Showing results 1 to 20 of 56.
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  1. Banisch, Ralf; Hartmann, Carsten: A sparse Markov chain approximation of LQ-type stochastic control problems (2016)
  2. Gogolinska, Anna; Jakubowski, Rafal; Nowak, Wieslaw: Petri nets formalism facilitates analysis of complex biomolecular structural data (2016)
  3. Casoni, E.; Jérusalem, A.; Samaniego, C.; Eguzkitza, B.; Lafortune, P.; Tjahjanto, D.D.; Sáez, X.; Houzeaux, G.; Vázquez, M.: Alya: computational solid mechanics for supercomputers (2015)
  4. Xue, Xu; Yongjun, Wang; Zhihong, Li: Folding of SAM-II riboswitch explored by replica-exchange molecular dynamics simulation (2015)
  5. Bujotzek, Alexander; Schütt, Ole; Nielsen, Adam; Fackeldey, Konstantin; Weber, Marcus: \ssfZIBgridfree: efficient conformational analysis by partition-of-unity coupling (2014)
  6. Pal, Anirban; Agarwala, Abhishek; Raha, Soumyendu; Bhattacharya, Baidurya: Performance metrics in a hybrid MPI-OpenMP based molecular dynamics simulation with short-range interactions (2014)
  7. Xu, Zhen; Hu, Guo-Hui; Wang, Zhi-Liang; Zhou, Zhe-Wei: Guided motion of short carbon nanotube driven by non-uniform electric field (2014)
  8. Arnold, Axel; Lenz, Olaf; Kesselheim, Stefan; Weeber, Rudolf; Fahrenberger, Florian; Roehm, Dominic; Košovan, Peter; Holm, Christian: ESPResSO 3.1: molecular dynamics software for coarse-grained models (2013)
  9. Escribano, Bruno; Akhmatskaya, Elena; Mujika, Jon I.: Combining stochastic and deterministic approaches within high efficiency molecular simulations (2013)
  10. Fackeldey, Konstantin; Bujotzek, Alexander; Weber, Marcus: A meshless discretization method for Markov state models applied to explicit water peptide folding simulations (2013)
  11. Jiao, Xiong; Yang, Lifeng; An, Meiwen; Chen, Weiyi: A modified amino acid network model contains similar and dissimilar weight (2013)
  12. Oden, J.Tinsley; Prudencio, Ernesto E.; Bauman, Paul T.: Virtual model validation of complex multiscale systems: applications to nonlinear elastostatics (2013)
  13. Villar, Juan A.; Andújar, Francisco J.; Sánchez, José L.; Alfaro, Francisco J.; Gámez, José A.; Duato, José: Obtaining the optimal configuration of high-radix combined switches (2013)
  14. Aktulga, Hasan Metin; Pandit, Sagar A.; Van Duin, Adri C.T.; Grama, Ananth Y.: Reactive molecular dynamics: numerical methods and algorithmic techniques (2012)
  15. Aktulga, H.M.; Fogarty, J.C.; Pandit, S.A.; Grama, A.Y.: Parallel reactive molecular dynamics: numerical methods and algorithmic techniques (2012)
  16. Fackeldey, Konstantin; Klimm, Martina; Weber, Marcus: A coarse graining method for the dimension reduction of the state space of biomolecules (2012)
  17. Gonnet, Pedro: A short note on the fast evaluation of dihedral angle potentials and their derivatives (2012)
  18. Lilkova, Elena; Nacheva, Genoveva; Petkov, Peicho; Petkov, Petko; Markov, Stoyan; Ilieva, Nevena; Litov, Leandar: Metadynamics study of mutant human interferon-gamma forms (2012)
  19. Lima, Angélica Nakagawa; Philot, Eric Allison; Perahia, David; Braz, Antonio Sérgio Kimus; Scott, Luis P.B.: GANM: A protein-ligand docking approach based on genetic algorithm and normal modes (2012)
  20. Martins do Canto, A.M.T.; Carvalho, A.J.Palace; Ramalho, J.P.Prates; Loura, Luís M.S.: Molecular dynamics simulation of HIV fusion inhibitor T-1249: insights on peptide-lipid interaction (2012)

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Further publications can be found at: http://www.gromacs.org/Gromacs_papers