Patent ID: 7908129

Claim:
A method of simulating behaviour of a molecular system with m degrees of freedom over time comprising: a partial momentum refreshment operation performed by a computer and a molecular dynamics operation performed by a computer, wherein the partial momentum refreshment operation comprises: given a starting position q and a starting momentum p of the molecular system, partially refreshing the momentum to define refreshed momentum p′ using a noise vector u, where: ( u ′ p ′ ) = ( cos ⁡ ( ϕ ) sin ⁡ ( ϕ ) sin ⁡ ( ϕ ) - cos ⁡ ( ϕ ) ) ⁢ ( u p ) where p′, p: refreshed and current momentum, 0≦φ≦π/2, u′, u: new and current noise vectors, u=β −1/2 (q) 1/2 ξ, ξ i ˜N(0,1), i=1, . . . , m, N(0,1) denoting the normal distribution with zero mean and unit variance, : mass matrix, β=1/K B T where T is temperature; evaluating the shadow Hamiltonian Δt at position q and momentum p′; and accepting or rejecting the refreshed momentum p′ according to a Metropolis-type function and if p′ is accepted using p′ as the resulting momentum p and starting position q as the resulting position q or if it is rejected, using p as the resulting momentum p and starting position q as the resulting position; and wherein the molecular dynamics operation comprises: given a starting position q and starting momentum p of the molecular system, running a molecular dynamics simulation over a fixed number of iterations and obtaining new position q′ and refreshed momentum p′; evaluating the shadow Hamiltonian Δt at position q′ and momentum p′ after the molecular dynamics simulation; and accepting or rejecting the new system configuration produced by the molecular dynamics simulation according to a Metropolis-type function and, if the new system configuration is accepted, using q′ as the resulting position q and p′ as the resulting momentum p or, if it is rejected, using the original starting position q as the resulting position q and negating the original starting momentum p to give the resulting momentum p; wherein either the partial momentum refreshment or the molecular dynamics operation is a first operation of the method, and the resulting position and resulting momentum of the first operation provides the starting position q and starting momentum p for a next operation.