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 113 articles )

Showing results 1 to 20 of 113.
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  1. Mongelli, Guy Francis: Molecular dynamics simulations. Key operations in GROMACS (to appear) (2022)
  2. Teixeira, J. M.: taurenmd: A command-line interface for analysis of Molecular Dynamics simulations (2020) not zbMATH
  3. Zhao, Yu; Liang, Rong; Yang, Yiying; Lin, Songyi: The mechanism of pulsed electric field (PEF) targeting location on the spatial conformation of pine nut peptide (2020)
  4. Agrahari, Ashish Kumar; Doss, George Priya C.; Siva, R.; Magesh, R.; Zayed, Hatem: Molecular insights of the G2019S substitution in LRRK2 kinase domain associated with Parkinson’s disease: A molecular dynamics simulation approach (2019)
  5. Anupama, Rani; Lulu, Sajitha; Madhusmita, Rout; Vino, Sundararajan; Mukherjee, Amitava; Babu, Subramanian: Insights into the interaction of key biofilm proteins in \textitPseudomonasaeruginosa PAO1 with TiO(_2) nanoparticle: an \textitinsilico analysis (2019)
  6. Bai, Xiaolu; Chen, Xiaolin: Rational design, conformational analysis and membrane-penetrating dynamics study of Bac2A-derived antimicrobial peptides against gram-positive clinical strains isolated from pyemia (2019)
  7. Hopp-Hirschler, Manuel; Baz, Jörg; Hansen, Niels; Nieken, Ulrich: Generalized Fickian approach for phase separating fluid mixtures in smoothed particle hydrodynamics (2019)
  8. Hoshi, Takeo; Imachi, Hiroto; Kuwata, Akiyoshi; Kakuda, Kohsuke; Fujita, Takatoshi; Matsui, Hiroyuki: Numerical aspect of large-scale electronic state calculation for flexible device material (2019)
  9. Lei, Huan; Li, Jing; Gao, Peiyuan; Stinis, Panagiotis; Baker, Nathan A.: A data-driven framework for sparsity-enhanced surrogates with arbitrary mutually dependent randomness (2019)
  10. Long, Andrew W.; Ferguson, Andrew L.: Landmark diffusion maps (L-dMaps): accelerated manifold learning out-of-sample extension (2019)
  11. Motamedi, Mohsen; Sohail, Ayesha: A theoretical framework for the biophysics of tubulins (2019)
  12. Rout, Subhashree; Mahapatra, Rajani Kanta: \textitInsilico analysis of \textitplasmodiumfalciparum CDPK5 protein through molecular modeling, docking and dynamics (2019)
  13. van den Berg, E.: The Ocean Tensor Package (2019) not zbMATH
  14. Younes Nejahi; Mohammad Soroush Barhaghi; Jason Mick; Brock Jackman; Kamel Rushaidat; Yuanzhe Li; Loren Schwiebert; Jeffrey Potoff: GOMC: GPU Optimized Monte Carlo for the simulation of phase equilibria and physical properties of complex fluids (2019) not zbMATH
  15. Bou-Rabee, Nawaf; Sanz-Serna, J. M.: Geometric integrators and the Hamiltonian Monte Carlo method (2018)
  16. Gong, Li-Hua; He, Xiang-Tao; Tan, Ru-Chao; Zhou, Zhi-Hong: Single channel quantum color image encryption algorithm based on HSI model and quantum Fourier transform (2018)
  17. Hassan, Mubashir; Abbasi, Muhammad Athar; Aziz-ur-Rehman; Siddiqui, Sabahat Zahra; Hussain, Ghulam; Shah, Syed Adnan Ali; Shahid, Muhammad; Seo, Sung-Yum: Exploration of synthetic multifunctional amides as new therapeutic agents for Alzheimer’s disease through enzyme inhibition, chemoinformatic properties, molecular docking and dynamic simulation insights (2018)
  18. Quer, J.; Donati, L.; Keller, B. G.; Weber, M.: An automatic adaptive importance sampling algorithm for molecular dynamics in reaction coordinates (2018)
  19. Yang, Jianbin; Zhu, Guanhua; Tong, Dudu; Lu, Lanyuan; Shen, Zuowei: B-spline tight frame based force matching method (2018)
  20. Antonov, M. Yu.; Popinako, A. V.; Prokopiev, G. A.; Vasilyev, A. O.: Numerical modelling of ion transport in 5-HT3 serotonin receptor using molecular dynamics (2017)

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