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Outline:Flow chart for MD run for proteins in a solvent box from Gromacs manual Delete water molecules present in the input pdb file About pdb2gmx command and syntax About force field options Adding solvent option Generate .gro file and format About hydrogens added in the .gro file About editconf command and syntax Create a bounding box Shape and size of the bounding box
Flow chart for MD run for proteins in a solvent box from Gromacs manual Delete water molecules present in the input pdb file About pdb2gmx command and syntax About force field options Adding solvent option Generate .gro file and format About hydrogens added in the .gro file About editconf command and syntax Create a bounding box Shape and size of the bounding box
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