Molecular dynamics implementation cheat sheet
A cheat-sheet for implementing a molecular dynamics simulation
Source: "Nanosystems: Molecular Machinery, Manufacturing, and Computation"
Contents
[hide]- 1 The MM2 model (3.3.2.)
- 2 Bonds under large loads (beyond MM2) (3.3.3.)
- 3 Verlet Integration (not in Nanosystems)
- 4 MM2 vs MM3 (Chapter 3.3.2.g.)
- 5 Bond cleavage & radical coupling (3.4.2)
- 6 Nonbonded & large compression limits (3.3.3.b.)
- 7 Abstraction reactions (Chapter 3.4.3.)
- 8 Continuum models of van der Waals attraction (Chapter 3.5.1.)
- 9 Related
The MM2 model (3.3.2.)
Vs=12ks(r−r0)2[1−kcubic(r−r0)] … stretching (3.4)
Vθ=12kθ(θ−θ0)2[1+ksextic(θ−θ0)4] … bending (3.5)
ks⊥=kθ/r20 … per length angular stiffness ks⊥≈ks/20 at (r0,θ0) (3.6)
Vω=12[V1(1−cos(1ω))+V2(1−cos(2ω))+V3(1+cos(3ω))] … torsion (3.7)
Vvdw=ϵvdw[2.48×105exp(−12.5rrvdw0)−1.924(rrvdw0)−6] … vdW attraction & non-bonded Pauli repulsion (3.8)
Vsθ=ksθ(θ−θ0)[(rA−rA0)+(rB−rB0)] … stretch-bend interaction (3.9)
ks,C−C=440N/m — r0,C−C=111.3pm … (Table 3.2.)
kθ,C−C−C=450zJ/rad2 — θ0,C−C−C=1.911rad=109.47∘ … (Table 3.3.)
ϵvdw,Csp3=357yJ — rvdw,Csp3=190pm … well depth ϵvdw varies widely for other atoms (~10x) (Table 3.1.)
V1,C−C−C−C=1.39zJ, V2,C−C−C−C=1.88zJ, V3,C−C−C−C=0.65zJ … (Table 3.5.)
ksθ,C−C−C=1.2nN/rad … (Table 3.6.)
kcubic=?m−1 — ksextic=?rad−4
n…nano=10−9 — p…pico=10−12
z…zepto=10−21 — y…yocto=10−24
Bonds under large loads (beyond MM2) (3.3.3.)
Vmorse=De(1−exp[−β(r−r0)]2−1) … tensile (3.10)
Vlippincott=De[1−exp(−ksr0(r−r0)22Der)], r≥r0 … tensile – more accurate for larger distances (3.15)
For compressive loads Vvdw see (3.8) above Fvdw=−∂∂rVvdw … (3.16)
Note: Popular Lennard-Jones 6-12 potential is too steep in repulsive regime!
MM2 potential within 10% of experiment for 0.5rvdw (>100yJ repulsion) 🙂
β=√ks/(2De) … (3.13)
De≈D0+ℏ2√ks/μ=D0+ℏω2; μ=m1m2m1+m2 … (3.14)
D0 … potential well depth
De,C−C=556yJ — ks,C−C=440N/m — r0,C−C=152.3pm … (Table 3.8)
Verlet Integration (not in Nanosystems)
→x(t+Δt)=2→x(t)−→x(t−Δt)+→a(t)Δt2+O(Δt4)
→a(t)=m∇→xV(t)
MM2 vs MM3 (Chapter 3.3.2.g.)
★ MM2 prioritizes accuracy in energy and geometry
★ MM3 prioritizes accuracy of vibration frequencies
★ MM3 predicts greater angle-bending stiffness by ~1.5x or more
★ MM3 has a more complex functional form – e.g. it adds:
– stretch-torsion interaction, cubic bending, quartic stretching
★ MM3 has lower energies forces and stiffness in deep repulsive regime by ~10%
★ MM2 overall seems like a more conservative (safe side wrong) choice for diamondoid nanomachinery
Bond cleavage & radical coupling (3.4.2)
The Morse potential Vmorse can approximate homolytic reactions
Vanti−morse=12De(1+exp[−β(r−r0)]2−1) … unpaired spins (3.21)
But unpaired spins being the limiting factor in reaction rate should
typically be avoidable in piezomechanosynthesis.
See Nanosystems Chapter 8.4.3.b. Radical coupling and intersystem crossing.
Nonbonded & large compression limits (3.3.3.b.)
ks,vdw≈12.5rvdw0Fvdw≈3.5×1010m−1⋅Fvdw … (3.18)
Vvdw≈0.08rvdw0Fvdw≈2.9×10−11m⋅Fvdw …(3.19)
Abstraction reactions (Chapter 3.4.3.)
VLEPS extended London-Eyring-Polyano-Sato potential – details omitted here
Continuum models of van der Waals attraction (Chapter 3.5.1.)
Hamaker constant – details omitted here
Related
- Snapback – sideward bond bending stiffness is only 1/20th of radial bond stretching/compressing stiffness
- Energy, force, and stiffness
- Atomic orbitals