Here, we have presented several common challenges faced by scientists who perform biomolecular simulations. We provide this perspective for the benefit of new users entering the field and for seasoned experts to consider how they can amplify the robustness and accessibility of their work to enhance reproducibility and usability. This list of suggestions is by no means exhaustive, but should help alleviate many of the common problems encountered during the process of engaging in theoretical research. Several of these suggestions may also be useful in other computational domains beyond the force field-based biomolecular simulations in which the authors specialize.