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For polyvaline the topology file and the file with the solvated peptide coordinates are valsolv.psf and valsolv.pdb respectively. This means that water molecules must be randomly distributed with some density around a protein to fill the entire unit cell. In what follows the preparation of solvated polyvaline peptide is considered. Initial polyvaline peptide structure with no water around is contained in the file val0. pdb. Note that this file st.

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