Energy fluctuation is regarded as a fundamental characteristic of symplectic integration, even in long-term simulations. A systematic approach for developing symplectic integration involves discretising a variational principle rather than the corresponding Euler–Lagrange equations, which are the equations of motion. The resulting numerical method is referred to as a variational integrator (VI). In the current paper, we investigate how the selection of initial values and energy discretisation in VIs can affect the behaviour of energy fluctuation. Numerical simulation of several conservative systems suggests that the combination of energy and initial velocity discretisations, both of higher and the same order of accuracy, can amount to numerical energy behavior with smaller error.