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