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Outline:About solvent molecule files that can be added to the system Solvate command View the solvated system in VMD About mdp file About grompp command Generate tpr binary file Use dump command to read binary file Find out charge (qtot) on molecule from topology file Add ions with genion command Syntax for adding positive and negative ions
About solvent molecule files that can be added to the system Solvate command View the solvated system in VMD About mdp file About grompp command Generate tpr binary file Use dump command to read binary file Find out charge (qtot) on molecule from topology file Add ions with genion command Syntax for adding positive and negative ions
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