Ab Initio Path Integral Molecular Dynamics (AIPIMD)

AIPIMD simulation of double proton transfer in Watson-Crick AT base-pair model FI-FA at 300 K. Sampling of phase-space is restrained near the transition state via umbrella sampling. Only the less acidic (upper) proton and its bonded partners (N and O) experience the harmonic bias potential. Strong quantum nature of a nucleus is characterized by a strong delocalization. In this movie, the delocalization is represented by the spread of the beads, which is more pronounced for the protons (white color) than for the heavy atoms composing the skeleton (green: carbon, blue: nitrogen, red: oxygen).

Technical details: BLYP exchange-correlation Kohn-Sham density functional, Car-Parrinello normal-mode Path-Integral Molecular Dynamics, massive Nose-Hoover chain thermostated NVT-ensemble, Goedecker Pseudopotentials, 100 Ry cutoff, and Trotter number P = 16. The reaction coordinate for the umbrella sampling: difference in distance of upper proton to bonded N and O atoms.
For more info see http://www.cs.sandia.gov/~oavonli,
Path-Integrals: http://en.wikipedia.org/wiki/Path_integral_formulation,
Molecular dynamics: http://en.wikipedia.org/wiki/Molecular_dynamics,
Car-Parrinello MD:
http://en.wikipedia.org/wiki/Car-Parrinello
Density Functional Theory:
http://en.wikipedia.org/wiki/Density_functional_theory

Scientific software used:
CPMD for calculations (http://www.cpmd.org), vmd for visualization (http://www.ks.uiuc.edu/Research/vmd/) using scripts obtained from Axel Kohlmeyer.

Category:

Science & Technology

Tags:

• ab
• initio
• path
• integral
• molecular
• dynamics
• DFT
• Feynman
• umbrella
• sampling
• Chandler
• BLYP
• Car-Parrinello
• Watson-Crick
• DNA
• base
• pair