The basic idea of molecular dynamics depends on the solution of Newton’s equations of motion for individual particles (atoms, ions, and molecules) [15]. MDS predicts the properties of assemblies of molecules in terms of their structure and the microscopic interactions between them [15, 16]. The downloaded solved structures for SARS-CoV-2 and HCV RdRps (PDB ID: 7BTF and 2XI3, respectively) are prepared using PyMOL software. Water molecules and ions are removed (except the Zn+2 and Mg+2), while any redundant chains are excluded. Additionally, any missed Hydrogen atoms are added using PyMOL. The High-performance computing unit (Bib Alex) of the Bibliotheca Alexandrina, Alexandria, Egypt, is used to perform the MDS study under the project entitled 'Structural demystifying of some Hepatitis C Virus proteins; An in silico study.' Nanoscale Molecular Dynamics (NAMD 2.13) software is used in the MDS. Its viewer software VMD is used to prepare the input files and analyze the trajectories [15, 17]. CHARMM 36 force field is used in NAMD, and the TIP3P water model is employed [15, 18]. The periodic boundary conditions are used in simulating the system while the temperature is raised from 0 K up to 310 K gradually in the equilibration phase. One hundred nanoseconds MDS production runs are performed for both SARS-CoV-2 and HCV RdRps at the NVT ensemble. After docking, 20 ns MDS runs are performed for the protein-sofosbuvir complexes. Cluster analysis is performed utilizing Chimera software's default parameters (UCSF) [19].

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