Hi all, I have to simulate peptide with SPC water model.During the simulation trajectory peptide is some time going out of box through periodic boundary condition is there but physical prescence of solvent is not there, i mean if i have to extract water molecule within 3 angstrong cutoff of peptide then it is not possible in all trajectory because of some steps in which peptide is outside of box.I want to fix one of atom in a box so that all in a process of folding simulation peptide will remain inside of box. I will be thankful for any positive response.
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