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Outline:About unfavorable interactions after the addition of solvent and ions View the solvated system in VMD Set up energy minimization mdrun command Verbose option to view the process Parameters for energy minimization About .edr file and energy command Write the potential to an xvg file Open the xvg file in Grace/Qtgrace View the smooth decay in potential energy after energy minimization
About unfavorable interactions after the addition of solvent and ions View the solvated system in VMD Set up energy minimization mdrun command Verbose option to view the process Parameters for energy minimization About .edr file and energy command Write the potential to an xvg file Open the xvg file in Grace/Qtgrace View the smooth decay in potential energy after energy minimization
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