  To quantify the progress in development of algorithms and forcefields used in
molecular simulations, a method for the assessment of the sampling quality is
needed. We propose a general method to assess the sampling quality through the
estimation of the number of independent samples obtained from molecular
simulations. This method is applicable to both dynamic and nondynamic methods
and utilizes the variance in the populations of physical states to determine
the ESS. We test the correctness and robustness of our procedure in a variety
of systems--two-state toy model, all-atom butane, coarse-grained calmodulin,
all-atom dileucine and Met-enkaphalin.
  We also introduce an automated procedure to obtain approximate physical
states from dynamic trajectories: this procedure allows for sample--size
estimation for systems for which physical states are not known in advance.
