meld.system.gameld

GaMELD Implementation Module.

GaMELD combines Gaussian Accelerated Molecular Dynamics (GaMD) and MELD using a new threshold calculation.

References

  1. Caparotta, A. Perez, When MELD meets GaMD: Accelerating Biomolecular Landscape Exploration.

Functions

change_thresholds(step, system_runner, ...)

Change energy thresholds after cMD and GaMELD Equilibration

compute_energy_width(gamd_log_filename, ...)

Compute standard deviation of the potential energies.

new_thresholds(thresholds)

Compute new thresholds.