Since Density Functional Theory (DFT) came to existence, the computational nano science has became significant. The numerical calculations based on computers have focused on two main subject, computational accuracy and computational speed. In this work, we have compared Plane wave (PW) based Quantum Espresso Code and Atomic Orbitals (AO) based Siesta Code, which are both Open-Source, by performing the calculations of Black Phosphorene (BP)-Alanine molecule for the first time. Also we have found the binding energies of Adenine and Guanine molecules on the phosphorene to compare with previous results in the literature. Next, we have explored the difference between the codes and/or methodologies by analyzing computational speed, trying to decrease the consumed computational time without compromising calculation accuracy. The newer version of the suitable compiler yields to very promising results. Effective use of the cores and flags of the compiler have also a great impact on the computational time.