Keep It Flexible: Driving Macromolecular Rotary Motions in Atomistic Simulations with GROMACS

Kutzner, Carsten; Czub, Jacek; Grubmüller, Helmut;
  • Publisher: Figshare
  • Related identifiers: doi: 10.1021/ct100666v.s002, doi: 10.1021/ct100666v.s001
  • Subject: protein subunit | Macromolecular Rotary Motions | Developmental Biology | rotation potentials | simulation | rotation axis | axis rotation technique | axis approach | Computational Biology | Genetics | GROMACS 4.5 MD package | Cancer | Biophysics | Atomistic Simulations
    • FOR: 80699 Information Systems not elsewhere classified | 29999 Physical Sciences not elsewhere classified | 69999 Biological Sciences not elsewhere classified | 39999 Chemical Sciences not elsewhere classified
    arxiv: Quantitative Biology::Subcellular Processes | Quantitative Biology::Biomolecules

We describe a versatile method to enforce the rotation of subsets of atoms, e.g., a protein subunit, in molecular dynamics (MD) simulations. In particular, we introduce a “flexible axis” technique that allows realistic flexible adaptions of both the rotary subunit as we... View more
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