Algorithm 2.

Real-space non-bonded interaction kernel used for GENESIS 1.0–1.3

do ij = 1, M

icel = cell_index(1,ij)

jcel = cell_index(2,ij)

do i = 1, N(icel)

force_temp(1:3) = 0.0

do k = 1, Neighbor(i,ij) Number of neighbors of i-th atm in icel-th cell

j = Neighbor_list(k,i,ij) Neighbor of i-th atom in icel-th cell

rij(1) = coord(1,i,icel)-coord(1,j,jcel)

rij(2) = coord(2,i,icel)-coord(2,j,jcel)

rij(3) = coord(3,i,icel)-coord(3,j,jcel)

dij = sqrt(rij(1)2+rij(1)2+rij(1)3)

calculate f (1:3):force component from given distance

force_temp(1) = force_temp(1) – f (1)

force_temp(2) = force_temp(2) – f (2)

force_temp(3) = force_temp(3) – f (3)

force(1,j,jcel) = force(1,j,jcel) + f (1)

force(2,j,jcel) = force(2,j,jcel) + f (2)

force(3,j,jcel) = force(3,j,jcel) + f (3)

end do

force(1,i,icel) = force(1,i,icel) + force_temp(1)

force(2,i,icel) = force(2,i,icel) + force_temp(2)

force(3,i,icel) = force(3,i,icel) + force_temp(3)

end do

end do