Sigmoid Accelerated Molecular Dynamics: An Efficient Enhanced Sampling Method for Biosystems

Gaussian accelerated molecular dynamics (GaMD) is recognized as a popular enhanced sampling method for tackling longstanding challenges in biomolecular simulations. Inspired by GaMD, Sigmoid accelerated molecular dynamics (SaMD) is proposed in this work by adding a Sigmoid boost potential to improve the balance between the highest acceleration and accurate reweighting. Compared with GaMD, SaMD extends the accessible time scale and improves the computational efficiency as tested in three tasks. In the alanine dipeptide task, SaMD can produce the free energy landscape with better accuracy and efficiency. In the chignolin folding task, the estimated Gibbs free energy difference can converge to the experimental value similar to 30% faster. In the protein-ligand binding task, the bound conformations are closer to the crystal structure with a minimal ligand root-mean-square deviation of 1.7 angstrom. The binding of the ligand XK263 to the HIV protease is reproduced by SaMD in similar to 60% less simulation time.