BIO0
Biomolecular Simulation
Xavier Daura
- 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).