Molecular dynamics implementation cheat sheet

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A cheat-sheet for implementing a molecular dynamics simulation
Source: "Nanosystems: Molecular Machinery, Manufacturing, and Computation"

The MM2 model (3.3.2.)

Vs=12ks(rr0)2[1kcubic(rr0)] … stretching (3.4)
Vθ=12kθ(θθ0)2[1+ksextic(θθ0)4] … bending (3.5)
ks=kθ/r20 … per length angular stiffness ksks/20 at (r0,θ0) (3.6)
Vω=12[V1(1cos(1ω))+V2(1cos(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(θθ0)[(rArA0)+(rBrB0)] … stretch-bend interaction (3.9)


ks,CC=440N/mr0,CC=111.3pm … (Table 3.2.)
kθ,CCC=450zJ/rad2θ0,CCC=1.911rad=109.47 … (Table 3.3.)
ϵvdw,Csp3=357yJrvdw,Csp3=190pm … well depth ϵvdw varies widely for other atoms (~10x) (Table 3.1.)
V1,CCCC=1.39zJ, V2,CCCC=1.88zJ, V3,CCCC=0.65zJ … (Table 3.5.)
ksθ,CCC=1.2nN/rad … (Table 3.6.)
kcubic=?m1ksextic=?rad4

nnano=109ppico=1012
zzepto=1021yyocto=1024

Bonds under large loads (beyond MM2) (3.3.3.)

Vmorse=De(1exp[β(rr0)]21) … tensile (3.10)
Vlippincott=De[1exp(ksr0(rr0)22Der)],  rr0 … 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)
DeD0+2ks/μ=D0+ω2;  μ=m1m2m1+m2 … (3.14)
D0 … potential well depth
De,CC=556yJks,CC=440N/mr0,CC=152.3pm … (Table 3.8)

Verlet Integration (not in Nanosystems)

x(t+Δt)=2x(t)x(tΔt)+a(t)Δt2+O(Δt4)
a(t)=mxV(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
Vantimorse=12De(1+exp[β(rr0)]21) … 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,vdw12.5rvdw0Fvdw3.5×1010m1Fvdw … (3.18)
Vvdw0.08rvdw0Fvdw2.9×1011mFvdw …(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

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