Simulation input files and parameters for the study of VRL-associated S229T mutation in LMP1 protein

This dataset contains the essential input files and parameters used for the molecular dynamics (MD) simulations reported in the article titled "Molecular dynamics analysis of the Epstein-Barr virus-LMP1 protein S229T mutation associated with vitreoretinal lymphoma". This dataset contains the complete set of input files used for the Molecular Dynamics simulations described in the article "Molecular dynamics analysis of the Epstein-Barr virus-LMP1 protein S229T mutation associated with vitreoretinal lymphoma": Minimization Files: min1.in, min2.in (Energy minimization protocols). Equilibration Files: md1.in, md2.in (Heating and equilibration protocols). Production Files: production.in (Production MD run parameters). System Files: system.prmtop (Topology) and system.rst7 (Initial coordinates). Scripts: tleap_commands.in (System construction protocol). Methods: The system was parameterized using the ff14SB force field and solvated in a TIP3P water box. All simulations were performed following the protocols described in the methodology section of the article. Usage: These files are provided to ensure the reproducibility of our simulation results.