Molecular mechanics

E = Eb + Eq + Ew + Evdw + Eelectrostatic

Eb = 0.5 kb(r-r0)2

Eq = 0.5 kq(q - q0)2

Ew = kw [ 1 + cos( n w - l)]

Evdw = A(r/rv0)-12 -B(r/rv0)-6

Eelectrostatic = qi qj / e r

(Ref)

F = m a

-dE/dri = Fi = mi d2ri/dt2 r = position (radius)

dt ~= 1 fs (1e-15 sec)

vi(t+dt/2) = vi(t-dt/2) + ai(t) dt update velocity & r

ri(t+dt) = ri(t)= v(t+dt/2)dt

b

q

w

a

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