Dynamic Processes: Lecture 1 Lecture Notes. MOLECULAR SIMULATIONS. ALL YOU (N)EVER WANTED TO KNOW Julia M. Goodfellow. WHY DO SIMULATIONS?. Numerical simulations fall between experiments and theoretical methods Where there are no available experimental data
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ALL YOU (N)EVER WANTED TO KNOW
Julia M. Goodfellow
Numerical simulations fall between experiments and theoretical methods
(1) X-RAY refinement
(2) NMR - structure determination from NOEs.
Optimization of models
(1) conformation in solution
(2) conformation of complex
atomistic representation (x,y,z,vx,vy,vz) and
thermodynamics ( macroscopic parameters such as heat capacity)
For many body systems - lots of microstates consistent with a given set of conditions (Temp, Pressure, Volume, Natoms)
Experimental measurements are an average over these states.
Simulations - find trajectory through all possible states and calculate average
Bond deformation, Bond Angle deform.,
Torsion angles, improper torsion, cross-terms
van der Waals, electrostatics, 1-4 electrostatics
Initial Model/Set Up
Analysis and Validation
(A) environmental effects on peptide stability: role of solvents in stabilising/ destabilising secondary structure
(B) conformation of chemically modified dnas
Protein folding/unfolding - solvent insertion into cavities; stability and unfolding of different protein architecture
development of systematic protocols for assessing simulations