Molecular Modelling - Lecture 3

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Presentation transcript:

Molecular Modelling - Lecture 3 Molecular Dynamics

Molecular Dynamics Computational approach to statistical mechanics beyond the static view of the molecule dynamic motions can explain the wide range of thermally accessible states and thereby connect structure and function Many different methods and sampling approaches to deal with the sampling problem 1 fs timestep means one million steps for a ns

Molecular Dynamics - Initial System Settings Structure Solvation water and salt ions Ensemble - NVE (microcanonical ensemble), NVT, NPT ... velocity initial velocity vector is set randomly so that the total kinetic energy of the system corresponds to the expected value at the target temperature set velocities from a Gaussian distribution Equilibration exchange between kinteic and potential energies stable when both terms, and total energy, converge to fluctuate about a value

Periodic Boundary Conditions Model system placed in unit cell and considered to have infinitely many images in space Any space-filling polyhedra cubic hexagonal prism truncated octahedrao rhombic dodecahedra

Reducing the Computational Cost Non-bonded interactions most time-consuming part of a simulation N2 Truncating Long-Range forces and the minimum image convention : Interaction for a molecule i are only counted between it and it’s closest image Simple cut-off truncation of potential creates problems with consistent potential and force

Truncating Long-Range forces and the minimum image convention Switching Use smoothing functions to smoothly switch off the interaction between a “cut-on” and a “cut-off” distance.

Truncating Long-Range forces and the minimum image convention Shifting alters function more gradually over entire range

Truncating Long-Range forces and the minimum image convention atom-based or group-based

MD - simple application: Simulated Annealing special case of either MD (`quenched' MD) or MC simulation, in which the temperature is gradually reduced during the simulation. Often, the system is first heated and then cooled the system is given the opportunity to surmount energetic barriers in a search for conformations with energies lower than the local-minimum energy found by energy minimization. can lead to more realistic simulations of dynamics at low temperature more expensive than energy minimization.