LAMMPS for beginners - Sandia National Laboratories

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Rhodopsin photoisomerization simulation• 190 ns simulation– 40 ns in dark-adapted state (J. Mol. Biol., 333, 493, (2003))– 150 ns after photoisomerization• CHARMM <strong>for</strong>ce field• P 3 M full electrostatics• Parallel on ~40 processors; more than 1 ns simulation / day of real time• Shake, 2 fs time step, velocity Verlet integrator• Constant membrane surface area• System description– All atom representation– 99 DOPC lipids– 7441 TIP3P waters– 348 rhodopsin residues– 41,623 total atoms– L x =55 Å, L y =77 Å, L z =94-98 Å
Photoisomerization of retinalDihedralremains intrans duringsubsequent150 ns ofrelaxation40-ns simulation indark-adapted stateεδHNγβ14α1512 111310 92011-cis retinal8191876541713 2Isomerization occurswithin 200 fs.16εδHNγβα14121315 2010119"all-trans" retinal1881935 4 26 116717
Page 2 and 3: A brief introduction to MD• MD: m
Page 4 and 5: MD in the Middle• Quantum mechani
Page 6 and 7: Classical MD in Parallel• MD is i
Page 8 and 9: A brief introduction to LAMMPSLAMMP
Page 10 and 11: How to get help with LAMMPS1. Excel
Page 12 and 13: Easily add your own LAMMPS feature
Page 14 and 15: Particle-mesh Methods for Coulombic
Page 16 and 17: Time Scale of Molecular Dynamics•
Page 18 and 19: Length Scale of Molecular Dynamics
Page 20 and 21: Melt Interface in NiAl• Mark Asta
Page 22 and 23: Shear Response of Cu Bicrystal• D
Page 24 and 25: 3d Membrane Self-Assembly• Mark S
Page 26 and 27: • Mike Brown (Sandia)Aspherical N
Page 28 and 29: LAMMPS’s Reactive Force Fields Ca
Page 30 and 31: [1000]MD Simulation of Shock-induce
Page 34 and 35: Transition in retinal’s interacti
Page 36 and 37: Radiation damage simulations► Rad
Page 38 and 39: Defect analysis► How the defect a
Page 40 and 41: Future areas of LAMMPS development

LAMMPS for beginners - Sandia National Laboratories

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