A Benchmark Test on the Leapfrog Integrator and its Middle Alternative

09 February 2021, Version 1
This content is a preprint and has not undergone peer review at the time of posting.


Benchmark tests of the integrators are performed on three systems. In the first two systems including the NMA system (ACE-NME) and an AT tract (A7-T7), the conformational change of dihedral flipping is simulated. In the last system malonaldehyde, the intramolecular proton transfer is investigated. The free energy simulation results obtained with two integrators for the equations of motion including the leapfrog (LF) integrator and the leapfrog-middle (LF-middle) scheme are tested extensively.


Free Energy Calculations
Umbrella Sampling
Dihedral Flipping
proton transfer
time steps
molecular dynamics
Semi-Empirical Quantum Mechanics
force field
Potential Energy Terms
Free Energy Landscape
Potential of mean force (PMF)
Weighted Histogram Analysis Method
Multi-scale Treatment
Base Flipping
Backbone Dihedral
Free Energy Profile


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