Classical molecular
dynamics is a computer simulation technique
that is in widespread use across many areas of science, from physics
and chemistry to materials, biology, and medicine. The method continues
to attract criticism due its oft-reported lack of reproducibility
which is in part due to a failure to submit it to reliable uncertainty
quantification (UQ). Here we show that the uncertainty arises from
a combination of (i) the input parameters and (ii) the intrinsic stochasticity
of the method controlled by the random seeds. To illustrate the situation,
we make a systematic UQ analysis of a widely used molecular dynamics
code (NAMD), applied to estimate binding free energy of a ligand-bound
to a protein. In particular, we replace the usually fixed input parameters
with random variables, systematically distributed about their mean
values, and study the resulting distribution of the simulation output.
We also perform a sensitivity analysis, which reveals that, out of
a total of 175 parameters, just six dominate the variance in the code
output. Furthermore, we show that binding energy calculations dampen
the input uncertainty, in the sense that the variation around the
mean output free energy is less than the variation around the mean
of the assumed input distributions, if the output is ensemble-averaged
over the random seeds. Without such ensemble averaging, the predicted
free energy is five times more uncertain. The distribution of the
predicted properties is thus strongly dependent upon the random seed.
Owing to this substantial uncertainty, robust statistical measures
of uncertainty in molecular dynamics simulation require the use of
ensembles in all contexts.