Molecular Modelling - Lecture 3

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Molecular Modelling - Lecture 3

• Molecular Dynamics

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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

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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

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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

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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 its closest image
• Simple cut-off truncation of potential creates
  problems with consistent potential and force

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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.

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Truncating Long-Range forces and the minimum
image convention

• Shifting
• alters function more gradually over entire range

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Truncating Long-Range forces and the minimum
image convention

• atom-based or group-based

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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.