If one carries out a molecular simulation ofNparticlesusing periodic boundary conditions, linear momentum is conserved,and hence, the number of degrees of freedom is set to 3N-3. Inmost programs, this number of degrees of freedom is the defaultsetting. However, if one carries out a molecular simulation in anexternalfield, one needs to ensure that degrees of freedom arechanged from this default setting to 3N, as in an externalfield thevelocity of the center of mass can change. Using the correct degrees offreedom is important in calculating the temperature and in somealgorithms to simulate at constant temperature. For sufficiently largesystems, the difference between 3Nand 3N-3 is negligible.However, there are systems in which the comparison withexperimental data requires molecular dynamics simulations of asmall number of particles. In this work, we illustrate the effect of an incorrect setting of degrees of freedom in molecular dynamicsimulations studying the diffusion properties of guest molecules in nanoporous materials. We show that previously published resultshave reported a surprising diffusion dependence on the loading, which could be traced back to an incorrect setting of the degrees offreedom. As the correct settings are convoluted and counterintuitive in some of the most commonly used molecular dynamicsprograms, we carried out a systematic study on the consequences of the various commonly used (incorrect) settings. Our conclusionis that for systems smaller than 50 particles the results are most likely unreliable as these are either performed at an incorrecttemperature or the temperature is incorrectly used in some of the results. Furthermore, a novel and efficient method to calculatediffusion coefficients of guest molecules into nanoporous materials at zero-loading conditions is introduced