Section outline

◄6. PROTEINS: BETWEEN ORDER AND DISORDER
►8. DATA ANALYSIS AND MOLECULAR DYNAMICS: PCA AND COLLECTIVE COORDINATES

  • LECTURES N. 13, 14, 17 and 18

    lecture 18 was devoted to the setup of  a project on the comparison of the dynamical structure of native and mutated viral lysozymes

    initial conditions, integration schemes, force fields, integration schemes, thermostats

    biological energy scales/biological time scales/ timescales of protein motions

    protein folding in vivo (crowding) / in vitro

    free energy barriers control relaxation times

    protein disorder/protein order in the simulation (solid-like vs liquid-like motions)

    quantum mechanics vs Molecular Mechanics

    force fields: bonded + nonbonded parametrisation (see also lecture N. 3)

    energy minimisation and the protein folding problem (recent application of AI: ALPHA FOLD 2)

    typical observables in a protein MD simulation: RMSD(t), RMSF(t), Rg(t)

    structural superposition of proteins

    the problem of roto-translation subtraction

    symplectic integrators, Verlet's algorithm: remarks on the Liouville’s formulation of the discretized dynamics

    (Tsai2004,  Binder_Ciccotti1996.pdf, Schiller2008)

    Trotter product formula of operators

    CONTROLLING TEMPERATURE AND PRESSURE IN MD

    MD as generator of thermodynamical statistics, overview

    Liouville formulation of the MD, factorization

    Ensembles

    Constant temperature MD: quenches, Anderson Thermostat, Nosè-Hoover Thermostat

    Temperature Echo


    CB_23_24_PACK_7 



    • CB_23_24_PACK_7 File
      Students must
      Mark as done

      Slides and supplemtary materials for the core lectures in MD of proteins

◄6. PROTEINS: BETWEEN ORDER AND DISORDER
►8. DATA ANALYSIS AND MOLECULAR DYNAMICS: PCA AND COLLECTIVE COORDINATES