Simulation replicates and duration

User discussions
1

GROMACS version: 2024.4
GROMACS modification: No

  1. Due to the stochastic nature of MD simulations, the trajectories generated for replicates may differ. Is there any standard/recommended number of replicates to run?
  2. For simulations of a complex comprising a protein (400-500 residues) and a small molecule ligand (300-500 Da), is there a recommended duration of simulation and how do we know if it is sufficient?
    Thank you!