[gmx-users] peptide is going outside of box

kinshuk at chem.iitb.ac.in kinshuk at chem.iitb.ac.in
Wed Feb 27 13:46:51 CET 2008

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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