Lau_molecular modeling Flashcards
what are some interactions that contribute to the potential energy of a molecule? (4)
bond length/angle stretching, torsion angle rotation, van der waals interactions, electrostatic interactions
what is attractive part of van der waals interaction caused by
induced transient dipoles between nearby atoms
what does performing energy minimization entail in modeling?
alter starting geometry of the model in order to determine lowest possible energy state for it
what is time step limited by in modeling?
the highest-frequency motion that needs to be simulated. you should split this into at least 10 segments to attain constant velocity/acceleration
what are periodic boundary conditions?
where the system is in contact with itself on all sides, mitigates edge effects. in this simulation, atoms that exit one side return from the opposite side, Pac-man style
WTF to do with water molecules in simulation?
it’s hard, you can replace with a continuum dielectric that gives electrostatic screening
what are multiscale models?
models that incorporate quantum physics, classical physics and dielectric medium
what is the typical timescale for protein folding
us - s
what is the typical timescale for allosteric transitions
us - s
what is the typical timescale for unhindered side chain rotations
ps - ns
what is the typical timescale for covalent bond vibrations
less than 1 ps
what is umbrella sampling?
a type of free energy simulation, you want to map a free energy surface so you identify an order parameter that reports on this conformational change. You apply a restraining potential, record its distribution - then do this many times until you produce a free energy (potential of mean force PMF) along the distance between protein domains (E)
