CCP5 Summer School Advanced Seminar Content: Biomolecular Simulation (2017)

SSP5 Summer School Advanced Seminar Content: Biomolecular Simulation (2017)

Richard Henchman, Chris Cave-Ayland and Richard Bradshaw


Basic Course contents
School Timetable
Summer School Main Page
 

  • Advanced 1:
    Biomolecular force fields: AMBER, CHARMM, OPLS, GROMOS; derivation of force field parameters; soft-core potentials. (90 mins).
  • Advanced 2:
    Assessing equilibration; energy analysis; structural analysis; principle-component analysis; calculation of entropy. (60 mins)
  • Advanced 3:
    Replica-exchange molecular dynamics; weighted-histogram analysis. (60 mins)
  • Advanced 4:
    Computation of NMR observables: NOEs; J-coupling constants; order parameters; calculation of spectra from simulation. (60 mins)
  • Advanced Practical Sessions:
    Calculation of the liquid properties and free energy of hydration of butane; Analysis of the interaction between the N-terminal SH3 domain of Grb2 and a 15-residue peptide from Sos2 based on GROMOS. (6 hours).

 

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